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| align="center" | 1.0.0
| align="center" | 1.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mass screening of contigs for antimicrobial and virulence genes Homepage: https://github.com/tseemann/abricate URL: https://github.com/tseemann/abricate<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mass screening of contigs for antimicrobial and virulence genes Homepage: https://github.com/tseemann/abricate URL: https://github.com/tseemann/abricate<br /><br /><br /></div>
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| align="center" | [https://abseil.io/ abseil]
| align="center" | -
| align="center" | 20230125.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives. Homepage: https://abseil.io/ URL: https://abseil.io/<br /><br /><br /></div>
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| align="center" | [https://www.bcgsc.ca/platform/bioinfo/software/abyss abyss]
| align="center" | [https://www.bcgsc.ca/platform/bioinfo/software/abyss abyss]
| align="center" | bio
| align="center" | bio
| align="center" | 2.0.2, 2.2.5
| align="center" | 2.0.2, 2.2.5, 2.3.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler Homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss URL: https://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler Homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss URL: https://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio<br /><br /><br /></div>
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| align="center" | [http://afni.nimh.nih.gov/ afni]
| align="center" | [http://afni.nimh.nih.gov/ afni]
| align="center" | bio
| align="center" | bio
| align="center" | 20.3.05, 21.2.10, 22.1.12, 23.1.00, 23.1.08, 20180404
| align="center" | 20.3.05, 21.2.10, 22.1.12, 23.1.00, 23.1.08, 24.1.03, 20180404
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. Homepage: http://afni.nimh.nih.gov/ URL: http://afni.nimh.nih.gov/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. Homepage: http://afni.nimh.nih.gov/ Keyword:bio<br /><br /><br /></div>
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| align="center" | [http://www.alberta-fem.de/ alberta]
| align="center" | [http://www.alberta-fem.de/ alberta]
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| align="center" | 3.0.3
| align="center" | 3.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ALBERTA is an Adaptive multiLevel finite element toolbox using Bisectioning refinement and Error control by Residual Techniques for scientific Applications. Currently, ALBERTA works without problems on Linux PCs, DEC, HP, SGI, and SUN workstations. OpenGL (e.g. Mesa) is a plus, BLAS is a must. ALBERTA is freely distributed for research and education. Homepage: http://www.alberta-fem.de/ Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ALBERTA is an Adaptive multiLevel finite element toolbox using Bisectioning refinement and Error control by Residual Techniques for scientific Applications. Currently, ALBERTA works without problems on Linux PCs, DEC, HP, SGI, and SUN workstations. OpenGL (e.g. Mesa) is a plus, BLAS is a must. ALBERTA is freely distributed for research and education. Homepage: http://www.alberta-fem.de/ Keyword:phys<br /><br /><br /></div>
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| align="center" | [https://github.com/COMBINE-lab/alevin-fry alevin-fry]
| align="center" | -
| align="center" | 0.8.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding. Homepage: https://github.com/COMBINE-lab/alevin-fry URL: https://github.com/COMBINE-lab/alevin-fry<br /><br /><br /></div>
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| align="center" | [http://www.broadinstitute.org/software/allpaths-lg/blog/ allpaths-lg]
| align="center" | [http://www.broadinstitute.org/software/allpaths-lg/blog/ allpaths-lg]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT Homepage: https://github.com/ALPSCore/ALPSCore URL: https://github.com/ALPSCore/ALPSCore Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT Homepage: https://github.com/ALPSCore/ALPSCore URL: https://github.com/ALPSCore/ALPSCore Keyword:phys<br /><br /><br /></div>
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| align="center" | [http://ambermd.org/amber.html amber]
| align="center" | [https://ambermd.org/amber.html amber]
| align="center" | chem
| align="center" | chem
| align="center" | 18.10-18.11, 18.14-18.17, 20.9-20.15, 20.12-20.15
| align="center" | 18.10-18.11, 18.14-18.17, 20.9-20.15, 20.12-20.15, 22.5-23.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: http://ambermd.org/amber.html URL: http://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: https://ambermd.org/amber.html URL: https://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>
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| align="center" | [https://ambermd.org/AmberTools.php ambertools]
| align="center" | [https://ambermd.org/AmberTools.php ambertools]
| align="center" | -
| align="center" | -
| align="center" | 20, 21, 22, 23
| align="center" | 20, 21, 22, 23.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AmberTools consists of several independently developed packages that work well by themselves, and with Amber20 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Homepage: https://ambermd.org/AmberTools.php URL: https://ambermd.org/AmberTools.php<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Homepage: https://ambermd.org/AmberTools.php URL: https://ambermd.org/AmberTools.php<br /><br /><br /></div>
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| align="center" | [https://github.com/ampl/mp ampl-mp]
| align="center" | [https://github.com/ampl/mp ampl-mp]
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| align="center" | [https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus amrfinderplus]
| align="center" | [https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus amrfinderplus]
| align="center" | -
| align="center" | -
| align="center" | 3.11.18, 3.11.26
| align="center" | 3.11.18, 3.11.26, 3.12.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. Homepage: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus URL: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. Homepage: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus URL: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus<br /><br /><br /></div>
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| align="center" | [http://www.popgen.dk/angsd angsd]
| align="center" | [http://www.popgen.dk/angsd angsd]
| align="center" | bio
| align="center" | bio
| align="center" | 0.918, 0.929, 0.933, 0.935, 0.936, 0.939
| align="center" | 0.918, 0.929, 0.933, 0.935, 0.936, 0.939, 0.940
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd URL: http://www.popgen.dk/angsd Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd URL: http://www.popgen.dk/angsd Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://ant.apache.org/ ant]
| align="center" | [https://ant.apache.org/ ant]
| align="center" | tools
| align="center" | tools
| align="center" | 1.9.15, 1.10.8
| align="center" | 1.9.15, 1.10.8, 1.10.14
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. Homepage: https://ant.apache.org/ URL: https://ant.apache.org/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. Homepage: https://ant.apache.org/ URL: https://ant.apache.org/ Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://stnava.github.io/ANTs/ ants]
| align="center" | [https://stnava.github.io/ANTs/ ants]
| align="center" | vis
| align="center" | vis
| align="center" | 2.2.0, 2.3.2, 2.3.5, 2.4.4
| align="center" | 2.2.0, 2.3.2, 2.3.5, 2.4.4, 2.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. Homepage: https://stnava.github.io/ANTs/ URL: https://stnava.github.io/ANTs/ Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. Homepage: https://stnava.github.io/ANTs/ URL: https://stnava.github.io/ANTs/ Keyword:vis<br /><br /><br /></div>
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. Homepage: https://apptainer.org URL: https://apptainer.org<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. Homepage: https://apptainer.org URL: https://apptainer.org<br /><br /><br /></div>
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| align="center" | [http://mbio-serv2.mbioekol.lu.se/ARAGORN/ aragorn]
| align="center" | [http://www.ansikte.se/ARAGORN/ aragorn]
| align="center" | -
| align="center" | -
| align="center" | 1.2.38, 1.2.41
| align="center" | 1.2.38, 1.2.41
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: a program to detect tRNA genes and tmRNA genes in nucleotide sequences Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ URL: http://mbio-serv2.mbioekol.lu.se/ARAGORN/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: a program to detect tRNA genes and tmRNA genes in nucleotide sequences Homepage: http://www.ansikte.se/ARAGORN/ URL: http://www.ansikte.se/ARAGORN/<br /><br /><br /></div>
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| align="center" | [https://github.com/bcgsc/arcs arcs]
| align="center" | [https://github.com/bcgsc/arcs arcs]
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| align="center" | tools
| align="center" | tools
| align="center" | 2.13
| align="center" | 2.13
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. Homepage: http://argtable.sourceforge.net/ URL: http://argtable.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. Homepage: http://argtable.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://sourceforge.net/projects/actc arioc]
| align="center" | [https://sourceforge.net/projects/actc arioc]
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| align="center" | [https://github.com/opencollab/arpack-ng arpack-ng]
| align="center" | [https://github.com/opencollab/arpack-ng arpack-ng]
| align="center" | math
| align="center" | math
| align="center" | 3.5.0, 3.7.0, 3.8.0, 3.9.0
| align="center" | 3.5.0, 3.7.0, 3.8.0, 3.9.0, 3.9.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: https://github.com/opencollab/arpack-ng URL: https://github.com/opencollab/arpack-ng Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: https://github.com/opencollab/arpack-ng URL: https://github.com/opencollab/arpack-ng Keyword:math<br /><br /><br /></div>
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| align="center" | -
| align="center" | -
| align="center" | 3.7.3, 3.8.2, 3.9.0
| align="center" | 3.7.3, 3.8.2, 3.9.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices. Homepage: https://arrayfire.com/ URL: https://arrayfire.com/ Compatible modules: python/3.7, python/3.8, python/3.9 Extensions: arrayfire-3.6.20181017<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices. Homepage: https://arrayfire.com/ URL: https://arrayfire.com/<br /><br /><br /></div>
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| align="center" | [https://arrow.apache.org arrow]
| align="center" | [https://arrow.apache.org arrow]
| align="center" | tools
| align="center" | tools
| align="center" | 0.11.1, 0.15.1, 0.16.0, 0.17.1, 2.0.0, 4.0.0, 5.0.0, 7.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0
| align="center" | 0.11.1, 0.15.1, 0.16.0, 0.17.1, 2.0.0, 5.0.0, 7.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0, 14.0.0, 14.0.1, 15.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.6.3, python/3.7.4, python/3.8.0 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.11, python/3.10 Keyword:tools<br /><br /><br /></div>
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| align="center" | [http://downloads.asperasoft.com/ ascp]
| align="center" | [http://downloads.asperasoft.com/ ascp]
| align="center" | tools
| align="center" | tools
| align="center" | 3.5.4
| align="center" | 3.5.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ URL: http://downloads.asperasoft.com/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://aspect.geodynamics.org/ aspect]
| align="center" | [https://aspect.geodynamics.org/ aspect]
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| align="center" | chem
| align="center" | chem
| align="center" | 4.2.7_2
| align="center" | 4.2.7_2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ATOM is the name of a program originally written (circa 1982) by Sverre Froyen at the University of California at Berkeley, modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota, and currently maintained by Alberto Garcia, who added some features and made substantial structural changes to the April 1990 (5.0) Minnesota version while at Berkeley and elsewhere. Homepage: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html URL: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ATOM is the name of a program originally written (circa 1982) by Sverre Froyen at the University of California at Berkeley, modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota, and currently maintained by Alberto Garcia, who added some features and made substantial structural changes to the April 1990 (5.0) Minnesota version while at Berkeley and elsewhere. Homepage: https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/downloads.html Keyword:chem<br /><br /><br /></div>
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| align="center" | [http://atomicrex.gitlab.io/atomicrex/ atomicrex]
| align="center" | [http://atomicrex.gitlab.io/atomicrex/ atomicrex]
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| align="center" | 1.1.2
| align="center" | 1.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AutoDock Vina is an open-source program for doing molecular docking. Homepage: http://vina.scripps.edu/index.html URL: http://vina.scripps.edu/index.html Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AutoDock Vina is an open-source program for doing molecular docking. Homepage: http://vina.scripps.edu/index.html URL: http://vina.scripps.edu/index.html Keyword:chem<br /><br /><br /></div>
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| align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-bacio/ bacio]
| align="center" | -
| align="center" | 2.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This library performs binary I/O for the NCEP models, processing unformatted byte-addressable data records, and transforming the little endian files and big endian files. This is part of the NCEPLIBS project. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-bacio/ URL: https://github.com/NOAA-EMC/NCEPLIBS-bacio/<br /><br /><br /></div>
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| align="center" | [http://bamm-project.org/ bamm]
| align="center" | [http://bamm-project.org/ bamm]
| align="center" | bio
| align="center" | bio
| align="center" | 2.5.0
| align="center" | 2.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. Homepage: http://bamm-project.org/ URL: http://bamm-project.org/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. Homepage: http://bamm-project.org/ Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://github.com/pezmaster31/bamtools bamtools]
| align="center" | [https://github.com/pezmaster31/bamtools bamtools]
| align="center" | bio
| align="center" | bio
| align="center" | 2.4.1, 2.5.1
| align="center" | 2.4.1, 2.5.1, 2.5.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. Homepage: https://github.com/pezmaster31/bamtools URL: https://github.com/pezmaster31/bamtools Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. Homepage: https://github.com/pezmaster31/bamtools URL: https://github.com/pezmaster31/bamtools Keyword:bio<br /><br /><br /></div>
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| align="center" | bio
| align="center" | bio
| align="center" | 1.0.14
| align="center" | 1.0.14
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. Homepage: http://genome.sph.umich.edu/wiki/BamUtil URL: http://genome.sph.umich.edu/wiki/BamUtil Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. Homepage: http://genome.sph.umich.edu/wiki/BamUtil Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://sourceforge.net/projects/seqbarracuda/ barracuda]
| align="center" | [https://sourceforge.net/projects/seqbarracuda/ barracuda]
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| align="center" | [https://sourceforge.net/projects/bbmap/ bbmap]
| align="center" | [https://sourceforge.net/projects/bbmap/ bbmap]
| align="center" | bio
| align="center" | bio
| align="center" | 37.36, 37.78, 38.86
| align="center" | 37.36, 37.78, 38.86, 39.06
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/ URL: https://sourceforge.net/projects/bbmap/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/ URL: https://sourceforge.net/projects/bbmap/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://samtools.github.io/bcftools/ bcftools]
| align="center" | [https://www.htslib.org/ bcftools]
| align="center" | bio
| align="center" | bio
| align="center" | 1.9, 1.10.2, 1.11, 1.13, 1.16
| align="center" | 1.9, 1.10.2, 1.11, 1.13, 1.16, 1.18, 1.19
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. In order to avoid tedious repetion, throughout this document we will use "VCF" and "BCF" interchangeably, unless specifically noted. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF work in all situations. Unindexed VCF and BCF and streams work in most, but not all situations. In general, whenever multiple VCFs are read simultaneously, they must be indexed and therefore also compressed. Homepage: https://samtools.github.io/bcftools/ URL: https://samtools.github.io/bcftools/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html bcl-convert]
| align="center" | -
| align="center" | 4.2.4, 4.2.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. Homepage: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html URL: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html<br /><br /><br /></div>
|-
|-
| align="center" | [https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html bcl2fastq2]
| align="center" | [https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html bcl2fastq2]
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| align="center" | [https://faculty.washington.edu/browning/beagle/beagle.html beagle]
| align="center" | [https://faculty.washington.edu/browning/beagle/beagle.html beagle]
| align="center" | -
| align="center" | -
| align="center" | 5.4
| align="center" | 5.4-240301
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Homepage: https://faculty.washington.edu/browning/beagle/beagle.html URL: https://faculty.washington.edu/browning/beagle/beagle.html<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Homepage: https://faculty.washington.edu/browning/beagle/beagle.html URL: https://faculty.washington.edu/browning/beagle/beagle.html<br /><br /><br /></div>
|-
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib URL: https://github.com/beagle-dev/beagle-lib Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib URL: https://github.com/beagle-dev/beagle-lib Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://beast2.org/ beast]
| align="center" | [http://beast2.org beast]
| align="center" | bio
| align="center" | bio
| align="center" | 1.8.2, 2.4.0, 2.6.0, 2.6.2, 2.6.3, 2.7.5
| align="center" | 1.8.2, 2.4.0, 2.6.0, 2.6.2, 2.6.3, 2.7.5
| Documentation: [[BEAST]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. - CC-Wiki: BEAST Homepage: http://beast2.org/ URL: http://beast2.org/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Homepage: http://beast2.org URL: http://beast2.org Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://bedops.readthedocs.io/en/latest/index.html bedops]
| align="center" | [http://bedops.readthedocs.io/en/latest/index.html bedops]
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| align="center" | [https://github.com/arq5x/bedtools2 bedtools]
| align="center" | [https://github.com/arq5x/bedtools2 bedtools]
| align="center" | bio
| align="center" | bio
| align="center" | 2.27.1, 2.28.0, 2.29.2, 2.30.0
| align="center" | 2.27.1, 2.28.0, 2.29.2, 2.30.0, 2.31.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Homepage: https://github.com/arq5x/bedtools2 URL: https://github.com/arq5x/bedtools2 Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Homepage: https://github.com/arq5x/bedtools2 URL: https://github.com/arq5x/bedtools2 Keyword:bio<br /><br /><br /></div>
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| align="center" | -
| align="center" | -
| align="center" | 1.03
| align="center" | 1.03
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. Homepage: https://sites.google.com/site/bgcsoftware/ URL: https://sites.google.com/site/bgcsoftware/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data. Homepage: https://sites.google.com/site/bgcsoftware/<br /><br /><br /></div>
|-
|-
| align="center" | [https://bitbucket.org/gavinband/bgen/src/default/ bgen]
| align="center" | [https://bitbucket.org/gavinband/bgen/src/default/ bgen]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorize sequences. This methodology is faster than alignment but does not provide mapping locations. BBT was initially intended to be used for pre-processing and QC applications like contamination detection, but is flexible to accommodate other purposes. This tool is intended to be a pipeline component to replace costly alignment steps. Homepage: https://github.com/bcgsc/biobloom URL: https://github.com/bcgsc/biobloom<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorize sequences. This methodology is faster than alignment but does not provide mapping locations. BBT was initially intended to be used for pre-processing and QC applications like contamination detection, but is flexible to accommodate other purposes. This tool is intended to be a pipeline component to replace costly alignment steps. Homepage: https://github.com/bcgsc/biobloom URL: https://github.com/bcgsc/biobloom<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.bioperl.org/ bioperl]
| align="center" | [https://bioperl.org/ bioperl]
| align="center" | bio
| align="center" | bio
| align="center" | 1.7.1, 1.7.5, 1.7.7, 1.7.8
| align="center" | 1.7.1, 1.7.5, 1.7.7, 1.7.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Homepage: http://www.bioperl.org/ Extensions: DBD::mysql-4.050, DBD::Pg-3.8.1, Devel::CheckLib-1.13, Devel::Cycle-1.12, IO::CaptureOutput-1.1104, PadWalker-2.3, Spiffy-0.46, Test::Base-0.89, Test::Memory::Cycle-1.06, Test::RequiresInternet-0.05, Test::Weaken-3.022000, Test::YAML-1.07, XML::DOM::XPath-0.14, XML::Filter::BufferText-1.01, XML::Parser-2.44, XML::RegExp-0.04, XML::XPathEngine-0.14, YAML-1.29 Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Homepage: https://bioperl.org/ URL: https://bioperl.org/ Extensions: Bio::Procedural-1.7.4, BioPerl-1.7.8, XML::DOM::XPath-0.14, XML::Writer-0.900 Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/BioPP/bpp-core biopp]
| align="center" | [https://github.com/BioPP/bpp-core biopp]
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| align="center" | [http://www.bioinformatics.babraham.ac.uk/projects/bismark/ bismark]
| align="center" | [http://www.bioinformatics.babraham.ac.uk/projects/bismark/ bismark]
| align="center" | -
| align="center" | -
| align="center" | 0.22.1, 0.22.3
| align="center" | 0.22.1, 0.22.3, 0.24.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tool to map bisulfite converted sequence reads and determine cytosine methylation states Homepage: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ URL: http://www.bioinformatics.babraham.ac.uk/projects/bismark/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A tool to map bisulfite converted sequence reads and determine cytosine methylation states Homepage: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ URL: http://www.bioinformatics.babraham.ac.uk/projects/bismark/<br /><br /><br /></div>
|-
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| align="center" | math
| align="center" | math
| align="center" | 1.1
| align="center" | 1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. Homepage: http://www.netlib.org/blacs/ URL: http://www.netlib.org/blacs/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. Homepage: http://www.netlib.org/blacs/ Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/PacificBiosciences/blasr blasr]
| align="center" | [https://github.com/PacificBiosciences/blasr blasr]
| align="center" | bio
| align="center" | bio
| align="center" | 5.3.0, 5.3.3
| align="center" | 5.3.0, 5.3.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. Homepage: https://github.com/PacificBiosciences/blasr Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PacBioi long read aligner Homepage: https://github.com/PacificBiosciences/blasr URL: https://github.com/PacificBiosciences/blasr Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/PacificBiosciences/blasr_libcpp blasr_libcpp]
| align="center" | [https://github.com/PacificBiosciences/blasr_libcpp blasr_libcpp]
| align="center" | bio
| align="center" | bio
| align="center" | 5.3.4, 20170426
| align="center" | 5.3.4, 20170426
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences Homepage: https://github.com/PacificBiosciences/blasr_libcpp URL: https://github.com/PacificBiosciences/blasr_libcpp Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences Homepage: https://github.com/PacificBiosciences/blasr_libcpp Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://blast.ncbi.nlm.nih.gov/ blast]
| align="center" | [http://blast.ncbi.nlm.nih.gov/ blast]
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| align="center" | [https://blast.ncbi.nlm.nih.gov/ blast+]
| align="center" | [https://blast.ncbi.nlm.nih.gov/ blast+]
| align="center" | bio
| align="center" | bio
| align="center" | 2.7.1, 2.8.1, 2.9.0, 2.10.0, 2.10.1, 2.11.0, 2.12.0, 2.13.0
| align="center" | 2.7.1, 2.8.1, 2.9.0, 2.10.0, 2.10.1, 2.11.0, 2.12.0, 2.13.0, 2.14.1
| Documentation: [[BLAST]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. Homepage: https://blast.ncbi.nlm.nih.gov/ URL: https://blast.ncbi.nlm.nih.gov/ Keyword:bio<br /><br /><br /></div>
| Documentation: [[BLAST]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. Homepage: https://blast.ncbi.nlm.nih.gov/ URL: https://blast.ncbi.nlm.nih.gov/ Keyword:bio<br /><br /><br /></div>
|-
|-
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| align="center" | [https://www.blender.org/ blender]
| align="center" | [https://www.blender.org/ blender]
| align="center" | vis
| align="center" | vis
| align="center" | 2.79b, 2.92.0, 3.6.0
| align="center" | 2.79b, 2.92.0, 3.6.0, 4.0.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. Homepage: https://www.blender.org/ URL: https://www.blender.org/ Compatible modules: python/3.7, python/3.8 Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. Homepage: https://www.blender.org/ URL: https://www.blender.org/ Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/flame/blis/ blis]
| align="center" | [https://github.com/flame/blis/ blis]
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| align="center" | phys
| align="center" | phys
| align="center" | 1.2.5
| align="center" | 1.2.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. Homepage: http://www.icams.de/content/departments/cmat/boltztrap/ URL: http://www.icams.de/content/departments/cmat/boltztrap/ Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. Homepage: http://www.icams.de/content/departments/cmat/boltztrap/ Keyword:phys<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.boost.org/ boost]
| align="center" | [https://www.boost.org/ boost]
| align="center" | tools
| align="center" | tools
| align="center" | 1.54.0, 1.60.0, 1.65.1, 1.66.0, 1.68.0, 1.72.0, 1.76.0, 1.80.0
| align="center" | 1.54.0, 1.60.0, 1.65.1, 1.66.0, 1.68.0, 1.72.0, 1.76.0, 1.80.0, 1.82.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.boost.org/ boost-build]
| align="center" | [https://www.boost.org/ boost-build]
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| align="center" | [https://www.boost.org/ boost-mpi]
| align="center" | [https://www.boost.org/ boost-mpi]
| align="center" | tools
| align="center" | tools
| align="center" | 1.68.0, 1.72.0, 1.80.0
| align="center" | 1.68.0, 1.72.0, 1.80.0, 1.82.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/ URL: https://www.boost.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://bowtie-bio.sourceforge.net/index.shtml bowtie]
| align="center" | [http://bowtie-bio.sourceforge.net/index.shtml bowtie]
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| align="center" | [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2]
| align="center" | [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2]
| align="center" | bio
| align="center" | bio
| align="center" | 2.3.4.3, 2.3.5, 2.3.5.1, 2.4.1, 2.4.2, 2.4.4, 2.5.1
| align="center" | 2.3.4.3, 2.3.5, 2.3.5.1, 2.4.1, 2.4.2, 2.4.4, 2.5.1, 2.5.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml URL: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Keyword:bio<br /><br /><br /></div>
|-
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads Homepage: http://gmt.genome.wustl.edu/packages/breakdancer Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads Homepage: http://gmt.genome.wustl.edu/packages/breakdancer Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/barricklab/breseq breseq]
| align="center" | [https://barricklab.org/breseq breseq]
| align="center" | -
| align="center" | -
| align="center" | 0.33.2, 0.35.2, 0.36.1
| align="center" | 0.33.2, 0.35.2, 0.36.1, 0.38.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data. It is intended for haploid microbial genomes (&lt;20 Mb). breseq is a command line tool implemented in C++ and R. Homepage: https://github.com/barricklab/breseq<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: breseq is a computational pipeline for the analysis of short-read re-sequencing data Homepage: https://barricklab.org/breseq URL: https://barricklab.org/breseq<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/google/brotli brotli]
| align="center" | [https://github.com/google/brotli brotli]
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| align="center" | 1.0.9
| align="center" | 1.0.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932. Homepage: https://github.com/google/brotli URL: https://github.com/google/brotli<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932. Homepage: https://github.com/google/brotli URL: https://github.com/google/brotli<br /><br /><br /></div>
|-
| align="center" | [https://github.com/google/brunsli/ brunsli]
| align="center" | -
| align="center" | 0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Brunsli is a lossless JPEG repacking library. Homepage: https://github.com/google/brunsli/ URL: https://github.com/google/brunsli/<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/bcgsc/btllib btllib]
| align="center" | [https://github.com/bcgsc/btllib btllib]
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| align="center" | 1.6.2
| align="center" | 1.6.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioinformatics Technology Lab common code library Homepage: https://github.com/bcgsc/btllib URL: https://github.com/bcgsc/btllib<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioinformatics Technology Lab common code library Homepage: https://github.com/bcgsc/btllib URL: https://github.com/bcgsc/btllib<br /><br /><br /></div>
|-
| align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-bufr/ bufr]
| align="center" | -
| align="center" | 12.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NCEPLIBS-bufr library contains routines and utilites for working with the WMO BUFR format. It is part of the NCEPLIBS project. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-bufr/ URL: https://github.com/NOAA-EMC/NCEPLIBS-bufr/<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB bufrlib]
| align="center" | [https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB bufrlib]
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| align="center" | bio
| align="center" | bio
| align="center" | 0.7.15, 0.7.17
| align="center" | 0.7.15, 0.7.17
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Homepage: http://bio-bwa.sourceforge.net/ URL: http://bio-bwa.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Homepage: http://bio-bwa.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/bwa-mem2/bwa-mem2 bwa-mem2]
| align="center" | [https://github.com/bwa-mem2/bwa-mem2 bwa-mem2]
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| align="center" | bio
| align="center" | bio
| align="center" | 20151002
| align="center" | 20151002
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/ URL: http://seq.cs.iastate.edu/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CAP3 assembly program Homepage: http://seq.cs.iastate.edu/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://capnproto.org capnproto]
| align="center" | [https://capnproto.org capnproto]
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| align="center" | geo
| align="center" | geo
| align="center" | 4_0_a02
| align="center" | 4_0_a02
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Homepage: http://www.cesm.ucar.edu/models/ccsm4.0/ URL: http://www.cesm.ucar.edu/models/ccsm4.0/ Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Homepage: http://www.cesm.ucar.edu/models/ccsm4.0/ Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [http://weizhongli-lab.org/cd-hit/ cd-hit]
| align="center" | [http://weizhongli-lab.org/cd-hit/ cd-hit]
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| align="center" | [https://code.zmaw.de/projects/cdo cdo]
| align="center" | [https://code.zmaw.de/projects/cdo cdo]
| align="center" | geo
| align="center" | geo
| align="center" | 1.7.2, 1.9.5, 1.9.8, 1.9.10, 2.0.4, 2.0.5
| align="center" | 1.7.2, 1.9.5, 1.9.8, 1.9.10, 2.0.4, 2.0.5, 2.2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo URL: https://code.zmaw.de/projects/cdo Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo URL: https://code.zmaw.de/projects/cdo Keyword:geo<br /><br /><br /></div>
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|-
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| align="center" | bio
| align="center" | bio
| align="center" | 2.1.0
| align="center" | 2.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. Homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome URL: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. Homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/single-cell-genetics/cellsnp-lite cellsnp-lite]
| align="center" | [https://github.com/single-cell-genetics/cellsnp-lite cellsnp-lite]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge URL: https://github.com/infphilo/centrifuge Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge URL: https://github.com/infphilo/centrifuge Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://uscilab.github.io/cereal/ cereal]
| align="center" | [https://uscilab.github.io/cereal/ cereal]
| align="center" | -
| align="center" | -
| align="center" | 1.2.2, 1.3.0
| align="center" | 1.2.2, 1.3.0, 1.3.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. Homepage: http://uscilab.github.io/cereal/ URL: http://uscilab.github.io/cereal/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. Homepage: https://uscilab.github.io/cereal/ URL: https://uscilab.github.io/cereal/<br /><br /><br /></div>
|-
|-
| align="center" | [https://ceres-solver.googlesource.com/ceres-solver/ ceres-solver]
| align="center" | [https://ceres-solver.googlesource.com/ceres-solver/ ceres-solver]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It is a feature rich, mature and performant library which has been used in production at Google since 2010. Ceres Solver can solve two kinds of problems: - Non-linear Least Squares problems with bounds constraints. - General unconstrained optimization problems. Homepage: https://ceres-solver.googlesource.com/ceres-solver/ URL: https://ceres-solver.googlesource.com/ceres-solver/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems. It is a feature rich, mature and performant library which has been used in production at Google since 2010. Ceres Solver can solve two kinds of problems: - Non-linear Least Squares problems with bounds constraints. - General unconstrained optimization problems. Homepage: https://ceres-solver.googlesource.com/ceres-solver/ URL: https://ceres-solver.googlesource.com/ceres-solver/<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.cesm.ucar.edu/models/cesm1.2/ cesm]
| align="center" | [http://www.cesm.ucar.edu/models/cesm2/ cesm]
| align="center" | geo
| align="center" | geo
| align="center" | 1_2_2, 2.1.1, 2.1.3
| align="center" | 1_2_2, 2.1.1, 2.1.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/cesm1.2/ URL: http://www.cesm.ucar.edu/models/cesm1.2/ Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/cesm2/ URL: http://www.cesm.ucar.edu/models/cesm2/ Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [https://heasarc.gsfc.nasa.gov/docs/software/fitsio// cfitsio]
| align="center" | [http://heasarc.gsfc.nasa.gov/fitsio/ cfitsio]
| align="center" | vis
| align="center" | vis
| align="center" | 3.41, 3.42, 3.48, 3.49, 4.1.0
| align="center" | 3.41, 3.42, 3.48, 3.49, 4.1.0, 4.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: https://heasarc.gsfc.nasa.gov/docs/software/fitsio// URL: https://heasarc.gsfc.nasa.gov/docs/software/fitsio// Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: http://heasarc.gsfc.nasa.gov/fitsio/ URL: http://heasarc.gsfc.nasa.gov/fitsio/ Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download cfour]
| align="center" | chem
| align="center" | 2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Serial version of CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Muller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. CFOUR is not a commercial code. It is rather a program that is undergoing development; new techniques and improvements are constantly being made (mainly in the groups of John F. Stanton (until the end of 2016 at the University of Texas at Austin, USA, now at the Quantum Theory Project of the University of Florida at Gainesville, USA) and Juergen Gauss (Universitat Mainz, Germany)). For non-commercial purposes there is no charge to obtain CFOUR; one must simply sign a license agreement. http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download Homepage: http://www.cfour.de/ URL: http://www.cfour.de/ Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download cfour-mpi]
| align="center" | [http://slater.chemie.uni-mainz.de/cfour/index.php?n=Main.Download cfour-mpi]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. Homepage: https://github.com/SebWouters/CheMPS2 URL: https://github.com/SebWouters/CheMPS2 Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. Homepage: https://github.com/SebWouters/CheMPS2 URL: https://github.com/SebWouters/CheMPS2 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [http://circos.ca/documentation/ circos]
| align="center" | [http://www.circos.ca/ circos]
| align="center" | vis
| align="center" | vis
| align="center" | 0.69-6, 0.69-9
| align="center" | 0.69-6, 0.69-9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive. Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience. Homepage: http://circos.ca/documentation/ URL: http://circos.ca/documentation/ Extensions: Config::General-2.63, Font::TTF::Font-1.06, GD-2.71, IO-1.39, SVG-2.84, Text::Balanced-2.03 Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. Homepage: http://www.circos.ca/ URL: http://www.circos.ca/ Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://clang.llvm.org/ clang]
| align="center" | [https://clang.llvm.org/ clang]
| align="center" | tools
| align="center" | tools
| align="center" | 3.8.1, 3.9.0, 9.0.1, 11.0.0, 13.0.1
| align="center" | 3.8.1, 3.9.0, 9.0.1, 11.0.0, 13.0.1, 17.0.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. Homepage: https://clang.llvm.org/ URL: https://clang.llvm.org/ Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. Homepage: https://clang.llvm.org/ URL: https://clang.llvm.org/ Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://proj-clhep.web.cern.ch/proj-clhep/ clhep]
| align="center" | [https://proj-clhep.web.cern.ch/proj-clhep/ clhep]
| align="center" | math
| align="center" | math
| align="center" | 2.4.1.0, 2.4.1.2, 2.4.1.3, 2.4.4.0, 2.4.6.2
| align="center" | 2.4.1.0, 2.4.1.2, 2.4.1.3, 2.4.4.0, 2.4.6.2, 2.4.7.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. Homepage: https://proj-clhep.web.cern.ch/proj-clhep/ URL: https://proj-clhep.web.cern.ch/proj-clhep/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. Homepage: https://proj-clhep.web.cern.ch/proj-clhep/ URL: https://proj-clhep.web.cern.ch/proj-clhep/ Keyword:math<br /><br /><br /></div>
|-
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| align="center" | bio
| align="center" | bio
| align="center" | 1.2.4
| align="center" | 1.2.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms Homepage: http://www.clustal.org/omega/ URL: http://www.clustal.org/omega/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms Homepage: http://www.clustal.org/omega/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.cmake.org cmake]
| align="center" | [https://www.cmake.org cmake]
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| align="center" | bio
| align="center" | bio
| align="center" | 0.4.1
| align="center" | 0.4.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing Homepage: https://github.com/abyzovlab/CNVnator URL: https://github.com/abyzovlab/CNVnator Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads Homepage: https://github.com/abyzovlab/CNVnator URL: https://github.com/abyzovlab/CNVnator Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/cdr/code-server code-server]
| align="center" | [https://github.com/cdr/code-server code-server]
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| align="center" | [https://docs.nvidia.com/cuda/cusparselt/index.html cusparselt]
| align="center" | [https://docs.nvidia.com/cuda/cusparselt/index.html cusparselt]
| align="center" | -
| align="center" | -
| align="center" | 0.4.0.7
| align="center" | 0.4.0.7, 0.5.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix Homepage: https://docs.nvidia.com/cuda/cusparselt/index.html URL: https://docs.nvidia.com/cuda/cusparselt/index.html<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix Homepage: https://docs.nvidia.com/cuda/cusparselt/index.html URL: https://docs.nvidia.com/cuda/cusparselt/index.html<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/ComputeCanada/custom_ctypes/ custom-ctypes]
| align="center" | [https://github.com/ComputeCanada/custom_ctypes/ custom-ctypes]
| align="center" | -
| align="center" | -
| align="center" | 1.1
| align="center" | 1.1, 1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This repository is to try to fix discovery of libraries with Python's ctypes module. It changes the behavior of find_library to return absolute paths to shared objects rather than just the names. Homepage: https://github.com/ComputeCanada/custom_ctypes/ URL: https://github.com/ComputeCanada/custom_ctypes/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This repository is to try to fix discovery of libraries with Python's ctypes module. It changes the behavior of find_library to return absolute paths to shared objects rather than just the names. Homepage: https://github.com/ComputeCanada/custom_ctypes/ URL: https://github.com/ComputeCanada/custom_ctypes/<br /><br /><br /></div>
|-
|-
| align="center" | [https://developer.nvidia.com/cutensor cutensor]
| align="center" | [https://developer.nvidia.com/cutensor cutensor]
| align="center" | -
| align="center" | -
| align="center" | 1.5.0.3, 1.7.0.1
| align="center" | 1.5.0.3, 1.7.0.1, 2.0.0.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cuTENSOR is a high-performance CUDA library for tensor primitives. Homepage: https://developer.nvidia.com/cutensor URL: https://developer.nvidia.com/cutensor<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cuTENSOR is a high-performance CUDA library for tensor primitives. Homepage: https://developer.nvidia.com/cutensor URL: https://developer.nvidia.com/cutensor<br /><br /><br /></div>
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| align="center" | 2.0.3
| align="center" | 2.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DAMASK is a flexible and hierarchically structured model of material point behavior for the solution of elastoplastic boundary value problems along with damage and thermal physics. Homepage: https://damask.mpie.de/Home/WebHome URL: https://damask.mpie.de/Home/WebHome<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DAMASK is a flexible and hierarchically structured model of material point behavior for the solution of elastoplastic boundary value problems along with damage and thermal physics. Homepage: https://damask.mpie.de/Home/WebHome URL: https://damask.mpie.de/Home/WebHome<br /><br /><br /></div>
|-
| align="center" | [https://github.com/cmks/DAS_Tool das_tool]
| align="center" | -
| align="center" | 1.1.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Homepage: https://github.com/cmks/DAS_Tool URL: https://github.com/cmks/DAS_Tool Extensions: data.table-1.14.8, docopt-0.7.1, magrittr-2.0.3<br /><br /><br /></div>
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|-
| align="center" | [https://www.oracle.com/technetwork/products/berkeleydb db]
| align="center" | [https://www.oracle.com/technetwork/products/berkeleydb db]
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| align="center" | [https://github.com/rordenlab/dcm2niix dcm2niix]
| align="center" | [https://github.com/rordenlab/dcm2niix dcm2niix]
| align="center" | bio
| align="center" | bio
| align="center" | 1.0.20180622, 1.0.20200331
| align="center" | 1.0.20180622, 1.0.20200331, 1.0.20230411
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. Homepage: https://github.com/rordenlab/dcm2niix URL: https://github.com/rordenlab/dcm2niix Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. Homepage: https://github.com/rordenlab/dcm2niix URL: https://github.com/rordenlab/dcm2niix Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [https://dicom.offis.de/dcmtk dcmtk]
| align="center" | [https://dicom.offis.de/dcmtk dcmtk]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers. Homepage: https://dicom.offis.de/dcmtk URL: https://dicom.offis.de/dcmtk<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers. Homepage: https://dicom.offis.de/dcmtk URL: https://dicom.offis.de/dcmtk<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.allinea.com ddt-cpu]
| align="center" | [https://www.linaroforge.com ddt-cpu]
| align="center" | tools
| align="center" | tools
| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1
| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1, 23.1.1
| Documentation: [[ARM software]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining Arm MAP and Arm DDT. Homepage: http://www.allinea.com URL: http://www.allinea.com<br /><br /><br /></div>
| Documentation: [[ARM software]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining MAP and DDT. Homepage: https://www.linaroforge.com URL: https://www.linaroforge.com<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.allinea.com ddt-gpu]
| align="center" | [https://www.linaroforge.com ddt-gpu]
| align="center" | tools
| align="center" | tools
| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1
| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1, 23.1.1
| Documentation: [[ARM software]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining Arm MAP and Arm DDT, with support for CUDA. Homepage: http://www.allinea.com URL: http://www.allinea.com<br /><br /><br /></div>
| Documentation: [[ARM software]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Profiler and debugger, combining MAP and DDT, with support for CUDA. Homepage: https://www.linaroforge.com URL: https://www.linaroforge.com<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.dealii.org/ dealii]
| align="center" | [http://www.dealii.org/ dealii]
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| align="center" | [https://github.com/dellytools/delly/ delly]
| align="center" | [https://github.com/dellytools/delly/ delly]
| align="center" | -
| align="center" | -
| align="center" | 0.7.8, 0.8.5, 1.1.6
| align="center" | 0.7.8, 0.8.5, 1.1.6, 1.1.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Homepage: https://github.com/dellytools/delly/ URL: https://github.com/dellytools/delly/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. Homepage: https://github.com/dellytools/delly/ URL: https://github.com/dellytools/delly/<br /><br /><br /></div>
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| align="center" | [https://github.com/bbuchfink/diamond diamond]
| align="center" | [https://github.com/bbuchfink/diamond diamond]
| align="center" | bio
| align="center" | bio
| align="center" | 0.8.38, 0.9.8, 0.9.14, 0.9.22, 0.9.32, 0.9.36, 2.0.2, 2.0.4, 2.0.9, 2.0.13, 2.0.15, 2.1.6, 2.1.7
| align="center" | 0.8.38, 0.9.8, 0.9.14, 0.9.22, 0.9.32, 0.9.36, 2.0.2, 2.0.4, 2.0.9, 2.0.13, 2.0.15, 2.1.6, 2.1.7, 2.1.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Accelerated BLAST compatible local sequence aligner Homepage: https://github.com/bbuchfink/diamond URL: https://github.com/bbuchfink/diamond Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Accelerated BLAST compatible local sequence aligner Homepage: https://github.com/bbuchfink/diamond URL: https://github.com/bbuchfink/diamond Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://github.com/nanoporetech/dorado dorado]
| align="center" | [https://github.com/nanoporetech/dorado dorado]
| align="center" | -
| align="center" | -
| align="center" | 0.2.1, 0.2.2, 0.3.0
| align="center" | 0.2.1, 0.2.2, 0.3.0, 0.4.1, 0.4.3, 0.5.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Homepage: https://github.com/nanoporetech/dorado URL: https://github.com/nanoporetech/dorado<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Homepage: https://github.com/nanoporetech/dorado URL: https://github.com/nanoporetech/dorado<br /><br /><br /></div>
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| align="center" | tools
| align="center" | tools
| align="center" | 1.1.8, 2.0.7
| align="center" | 1.1.8, 2.0.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Homepage: https://www.microsoft.com/net/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications. Homepage: https://www.microsoft.com/net/ Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/google/double-conversion double-conversion]
| align="center" | [https://github.com/google/double-conversion double-conversion]
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| align="center" | 2.3.0, 3.1.4
| align="center" | 2.3.0, 3.1.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. If you use DSSP, please quote these two articles: 1) A series of PDB related databases for everyday needs. Wouter G Touw, Coos Baakman, Jon Black, Tim AH te Beek, E Krieger, Robbie P Joosten, Gert Vriend. Nucleic Acids Research 2015 January; 43(Database issue): D364-D368. 2) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers. 1983 22 2577-2637. PMID: 6667333; UI: 84128824. Homepage: https://swift.cmbi.umcn.nl/gv/dssp/ URL: https://swift.cmbi.umcn.nl/gv/dssp/ Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. If you use DSSP, please quote these two articles: 1) A series of PDB related databases for everyday needs. Wouter G Touw, Coos Baakman, Jon Black, Tim AH te Beek, E Krieger, Robbie P Joosten, Gert Vriend. Nucleic Acids Research 2015 January; 43(Database issue): D364-D368. 2) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers. 1983 22 2577-2637. PMID: 6667333; UI: 84128824. Homepage: https://swift.cmbi.umcn.nl/gv/dssp/ URL: https://swift.cmbi.umcn.nl/gv/dssp/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://ecbuild.readthedocs.io/ ecbuild]
| align="center" | -
| align="center" | 3.8.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems Homepage: https://ecbuild.readthedocs.io/ URL: https://ecbuild.readthedocs.io/<br /><br /><br /></div>
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| align="center" | [https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home eccodes]
| align="center" | [https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home eccodes]
| align="center" | geo
| align="center" | geo
| align="center" | 2.8.2, 2.15.0, 2.18.0, 2.19.0, 2.22.1, 2.25.0
| align="center" | 2.8.2, 2.15.0, 2.18.0, 2.19.0, 2.22.1, 2.25.0, 2.31.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). Homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home URL: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: cfgrib-0.9.10.1, eccodes-1.4.1 Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). Homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home URL: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home Compatible modules: python/3.10, python/3.11 Extensions: cfgrib-0.9.10.4, eccodes-1.6.1 Keyword:geo<br /><br /><br /></div>
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|-
| align="center" | [https://www.perl.org/ eclipse]
| align="center" | [https://www.perl.org/ eclipse]
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| align="center" | 4.6.0
| align="center" | 4.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eclipse is an integrated development environment (IDE) used in computer programming, and is the most widely used Java IDE.[6] It contains a base workspace and an extensible plug-in system for customizing the environment. Eclipse is written mostly in Java and its primary use is for developing Java applications, but it may also be used to develop applications in other programming languages via plug-ins, including: Ada, ABAP, C, C++, COBOL, D, Fortran, Haskell, JavaScript, Julia,[7] Lasso, Lua, NATURAL, Perl, PHP, Prolog, Python, R, Ruby (including Ruby on Rails framework), Rust, Scala, Clojure, Groovy, Scheme, and Erlang. It can also be used to develop documents with LaTeX (via a TeXlipse plug-in) and packages for the software Mathematica. Development environments include the Eclipse Java development tools (JDT) for Java and Scala, Eclipse CDT for C/C++, and Eclipse PDT for PHP, among others. - Homepage: https://www.perl.org/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eclipse is an integrated development environment (IDE) used in computer programming, and is the most widely used Java IDE.[6] It contains a base workspace and an extensible plug-in system for customizing the environment. Eclipse is written mostly in Java and its primary use is for developing Java applications, but it may also be used to develop applications in other programming languages via plug-ins, including: Ada, ABAP, C, C++, COBOL, D, Fortran, Haskell, JavaScript, Julia,[7] Lasso, Lua, NATURAL, Perl, PHP, Prolog, Python, R, Ruby (including Ruby on Rails framework), Rust, Scala, Clojure, Groovy, Scheme, and Erlang. It can also be used to develop documents with LaTeX (via a TeXlipse plug-in) and packages for the software Mathematica. Development environments include the Eclipse Java development tools (JDT) for Java and Scala, Eclipse CDT for C/C++, and Eclipse PDT for PHP, among others. - Homepage: https://www.perl.org/ Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://www.ncbi.nlm.nih.gov/books/NBK25501/ edirect]
| align="center" | -
| align="center" | 20.9.20231210
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases from a Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in a variety of formats. Homepage: https://www.ncbi.nlm.nih.gov/books/NBK25501/ URL: https://www.ncbi.nlm.nih.gov/books/NBK25501/<br /><br /><br /></div>
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|-
| align="center" | [https://github.com/dipetkov/eems eems]
| align="center" | [https://github.com/dipetkov/eems eems]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This repository contains an implementation of the EEMS method for analyzing and visualizing spatial population structure from geo-referenced genetic samples. EEMS uses the concept of effective migration to model the relationship between genetics and geography, and it outputs an estimated effective migration surface (hence, EEMS) - a visual representation of population structure that can highlight potential regions of higher-than-average and lower-than-average historic gene flow. Homepage: https://github.com/dipetkov/eems Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This repository contains an implementation of the EEMS method for analyzing and visualizing spatial population structure from geo-referenced genetic samples. EEMS uses the concept of effective migration to model the relationship between genetics and geography, and it outputs an estimated effective migration surface (hence, EEMS) - a visual representation of population structure that can highlight potential regions of higher-than-average and lower-than-average historic gene flow. Homepage: https://github.com/dipetkov/eems Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [https://eigen.tuxfamily.org/index.php?title=Main_Page eigen]
| align="center" | [https://eigen.tuxfamily.org eigen]
| align="center" | math
| align="center" | math
| align="center" | 3.2.2, 3.2.10, 3.3.2, 3.3.5, 3.3.7, 3.4.0
| align="center" | 3.2.2, 3.2.10, 3.3.2, 3.3.5, 3.3.7, 3.4.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: https://eigen.tuxfamily.org/index.php?title=Main_Page URL: https://eigen.tuxfamily.org/index.php?title=Main_Page Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: https://eigen.tuxfamily.org URL: https://eigen.tuxfamily.org Keyword:math<br /><br /><br /></div>
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|-
| align="center" | [http://www.hsph.harvard.edu/alkes-price/software/ eigensoft]
| align="center" | [http://www.hsph.harvard.edu/alkes-price/software/ eigensoft]
| align="center" | bio
| align="center" | bio
| align="center" | 7.2.1
| align="center" | 7.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Homepage: http://www.hsph.harvard.edu/alkes-price/software/ URL: http://www.hsph.harvard.edu/alkes-price/software/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Homepage: http://www.hsph.harvard.edu/alkes-price/software/ Keyword:bio<br /><br /><br /></div>
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| align="center" | [http://elastix.isi.uu.nl/ elastix]
| align="center" | [http://elastix.isi.uu.nl/ elastix]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC). Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry. After it's open source publication in 2005, the use and development of Elmer has become international. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM). Homepage: https://www.csc.fi/web/elmer URL: https://www.csc.fi/web/elmer<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC). Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry. After it's open source publication in 2005, the use and development of Elmer has become international. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM). Homepage: https://www.csc.fi/web/elmer URL: https://www.csc.fi/web/elmer<br /><br /><br /></div>
|-
|-
| align="center" | [https://elpa.rzg.mpg.de elpa]
| align="center" | [https://elpa.mpcdf.mpg.de/ elpa]
| align="center" | math
| align="center" | math
| align="center" | 2017.11.001, 2018.11.001, 2020.05.001
| align="center" | 2017.11.001, 2018.11.001, 2020.05.001, 2023.05.001
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigenvalue SoLvers for Petaflop-Applications . Homepage: https://elpa.rzg.mpg.de URL: https://elpa.rzg.mpg.de Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eigenvalue SoLvers for Petaflop-Applications. Homepage: https://elpa.mpcdf.mpg.de/ URL: https://elpa.mpcdf.mpg.de/ Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [https://wordpress.elsi-interchange.org/ elsi]
| align="center" | [https://wordpress.elsi-interchange.org/ elsi]
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| align="center" | [https://github.com/embree/embree embree]
| align="center" | [https://github.com/embree/embree embree]
| align="center" | -
| align="center" | -
| align="center" | 2.17.7, 3.11.0, 3.13.5
| align="center" | 2.17.7, 3.11.0, 3.13.5, 4.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. Homepage: https://github.com/embree/embree URL: https://github.com/embree/embree<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. Homepage: https://github.com/embree/embree URL: https://github.com/embree/embree<br /><br /><br /></div>
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| align="center" | [https://www.earthsystemcog.org/projects/esmf/ esmf]
| align="center" | [https://www.earthsystemcog.org/projects/esmf/ esmf]
| align="center" | geo
| align="center" | geo
| align="center" | 7.1.0r, 8.0.1, 8.2.0, 8.4.0
| align="center" | 7.1.0r, 8.0.1, 8.2.0, 8.4.0, 8.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. Homepage: https://www.earthsystemcog.org/projects/esmf/ URL: https://www.earthsystemcog.org/projects/esmf/ Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. Homepage: https://www.earthsystemcog.org/projects/esmf/ URL: https://www.earthsystemcog.org/projects/esmf/ Compatible modules: python/3.10, python/3.11 Extensions: esmpy-8.6.0 Keyword:geo<br /><br /><br /></div>
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|-
| align="center" | [https://github.com/espeak-ng/espeak-ng espeak-ng]
| align="center" | [https://github.com/espeak-ng/espeak-ng espeak-ng]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. Homepage: http://www.etsf.eu/resources/software/libraries_and_tools URL: http://www.etsf.eu/resources/software/libraries_and_tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. Homepage: http://www.etsf.eu/resources/software/libraries_and_tools URL: http://www.etsf.eu/resources/software/libraries_and_tools<br /><br /><br /></div>
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|-
| align="center" | [https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate exonerate]
| align="center" | [http://www.ebi.ac.uk/~guy/exonerate/ exonerate]
| align="center" | bio
| align="center" | bio
| align="center" | 2.4.0
| align="center" | 2.4.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate URL: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Homepage: http://www.ebi.ac.uk/~guy/exonerate/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://expat.sourceforge.net/ expat]
| align="center" | [https://libexpat.github.io expat]
| align="center" | tools
| align="center" | tools
| align="center" | 2.2.6, 2.2.9, 2.2.10, 2.4.1
| align="center" | 2.2.6, 2.2.9, 2.2.10, 2.4.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) Homepage: http://expat.sourceforge.net/ URL: http://expat.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) Homepage: https://libexpat.github.io URL: https://libexpat.github.io Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://pachterlab.github.io/eXpress express]
| align="center" | [https://pachterlab.github.io/eXpress express]
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| align="center" | [https://github.com/facebookresearch/faiss faiss]
| align="center" | [https://github.com/facebookresearch/faiss faiss]
| align="center" | -
| align="center" | -
| align="center" | 1.6.2, 1.6.5, 1.7.1, 1.7.3
| align="center" | 1.6.2, 1.6.5, 1.7.1, 1.7.3, 1.7.4, 1.8.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. Homepage: https://github.com/facebookresearch/faiss URL: https://github.com/facebookresearch/faiss Compatible modules: python/3.6.3, python/3.7.4, python/3.8.0<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Faiss is a library for efficient similarity search and clustering of dense vectors. It contains algorithms that search in sets of vectors of any size, up to ones that possibly do not fit in RAM. It also contains supporting code for evaluation and parameter tuning. Faiss is written in C++ with complete wrappers for Python/numpy. Some of the most useful algorithms are implemented on the GPU. Homepage: https://github.com/facebookresearch/faiss URL: https://github.com/facebookresearch/faiss Compatible modules: python/3.10, python/3.11<br /><br /><br /></div>
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|-
| align="center" | [https://github.com/PacificBiosciences/FALCON falcon]
| align="center" | [https://github.com/PacificBiosciences/FALCON falcon]
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| align="center" | [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc]
| align="center" | [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc]
| align="center" | bio
| align="center" | bio
| align="center" | 0.11.5, 0.11.8, 0.11.9, 0.12.0
| align="center" | 0.11.5, 0.11.8, 0.11.9, 0.12.0, 0.12.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. Homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Keyword:bio<br /><br /><br /></div>
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| align="center" | bio
| align="center" | bio
| align="center" | 0.2.0
| align="center" | 0.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage: https://github.com/rrwick/Filtlong URL: https://github.com/rrwick/Filtlong Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage: https://github.com/rrwick/Filtlong Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html fineradstructure]
| align="center" | [http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html fineradstructure]
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| align="center" | [https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release flexiblas]
| align="center" | [https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release flexiblas]
| align="center" | -
| align="center" | -
| align="center" | 3.0.4, 3.2.0
| align="center" | 3.0.4, 3.2.0, 3.3.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. Homepage: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release URL: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release Extensions: LAPACK-3.9.0<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. Homepage: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release URL: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release Extensions: LAPACK-3.11.0<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.flintlib.org/ flint]
| align="center" | [http://www.flintlib.org/ flint]
| align="center" | math
| align="center" | math
| align="center" | 2.5.2, 2.7.1, 2.9.0
| align="center" | 2.5.2, 2.7.1, 2.9.0, 3.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. Homepage: http://www.flintlib.org/ URL: http://www.flintlib.org/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. Homepage: http://www.flintlib.org/ URL: http://www.flintlib.org/ Keyword:math<br /><br /><br /></div>
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| align="center" | 16.1
| align="center" | 16.1
| Documentation: [[Ansys]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS Fluent software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications, ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Fluent covers a broad reach, including special models with capabilities to model in-cylinder combustion, aero-acoustics, turbomachinery and multiphase systems. Homepage: https://www.ansys.com/products/fluids/ansys-fluent Keyword:phys<br /><br /><br /></div>
| Documentation: [[Ansys]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS Fluent software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications, ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Fluent covers a broad reach, including special models with capabilities to model in-cylinder combustion, aero-acoustics, turbomachinery and multiphase systems. Homepage: https://www.ansys.com/products/fluids/ansys-fluent Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [https://github.com/HudsonAlpha/fmlrc2 fmlrc2]
| align="center" | -
| align="center" | 0.1.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FMLRC v2, based on the same methodology used by the original FMLRC. In benchmarks, the results between FMLRC v1 and v2 are nearly identical, but tests have shown that v2 uses approximately 50% of the run and CPU time compared to v1. Homepage: https://github.com/HudsonAlpha/fmlrc2 URL: https://github.com/HudsonAlpha/fmlrc2<br /><br /><br /></div>
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| align="center" | [https://fmm3d.readthedocs.io fmm3d]
| align="center" | [https://fmm3d.readthedocs.io fmm3d]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/ URL: http://fmtlib.net/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fmt (formerly cppformat) is an open-source formatting library. Homepage: http://fmtlib.net/ URL: http://fmtlib.net/<br /><br /><br /></div>
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|-
| align="center" | [https://sourceforge.net/projects/freepascal/ fpc]
| align="center" | [https://www.freepascal.org fpc]
| align="center" | tools
| align="center" | tools
| align="center" | 3.0.0, 3.2.2
| align="center" | 3.0.0, 3.2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A 32/64/16-bit Pascal compiler for Win32/64/CE, Linux, Mac OS X/iOS, FreeBSD, OS/2, Game Boy Advance, Nintendo NDS and DOS; semantically compatible with Delphi, Borland Pascal and Mac Pascal (partially) with extra features, e.g. operator overloading. Homepage: https://sourceforge.net/projects/freepascal/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Free Pascal is a mature, versatile, open source Pascal compiler. Homepage: https://www.freepascal.org URL: https://www.freepascal.org Keyword:tools<br /><br /><br /></div>
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| align="center" | [http://omics.informatics.indiana.edu/FragGeneScan/ fraggenescan]
| align="center" | [http://omics.informatics.indiana.edu/FragGeneScan/ fraggenescan]
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| align="center" | [https://www.gaia-gis.it/fossil/freexl/index freexl]
| align="center" | [https://www.gaia-gis.it/fossil/freexl/index freexl]
| align="center" | tools
| align="center" | tools
| align="center" | 1.0.3, 1.0.5
| align="center" | 1.0.3, 1.0.5, 2.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. Homepage: https://www.gaia-gis.it/fossil/freexl/index URL: https://www.gaia-gis.it/fossil/freexl/index Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. Homepage: https://www.gaia-gis.it/fossil/freexl/index URL: https://www.gaia-gis.it/fossil/freexl/index Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://www.fmrib.ox.ac.uk/fsl/ fsl]
| align="center" | [https://www.fmrib.ox.ac.uk/fsl/ fsl]
| align="center" | bio
| align="center" | bio
| align="center" | 6.0.1, 6.0.3, 6.0.4
| align="center" | 6.0.1, 6.0.3, 6.0.4, 6.0.7.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: https://www.fmrib.ox.ac.uk/fsl/ URL: https://www.fmrib.ox.ac.uk/fsl/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: https://www.fmrib.ox.ac.uk/fsl/ URL: https://www.fmrib.ox.ac.uk/fsl/ Keyword:bio<br /><br /><br /></div>
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Extract sequences from a fastx file given a subsequence or identifier Homepage: https://github.com/ctSkennerton/fxtract<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Extract sequences from a fastx file given a subsequence or identifier Homepage: https://github.com/ctSkennerton/fxtract<br /><br /><br /></div>
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|-
| align="center" | [https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2clib]
| align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-g2c g2clib]
| align="center" | geo
| align="center" | geo
| align="center" | 1.6.0
| align="center" | 1.6.0, 1.8.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder ('C' version). Homepage: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ URL: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This library contains C decoder/encoder routines for GRIB edition 2. This is part of the NCEPLIBS project. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-g2c URL: https://github.com/NOAA-EMC/NCEPLIBS-g2c Keyword:geo<br /><br /><br /></div>
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|-
| align="center" | [https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2lib]
| align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-g2/ g2lib]
| align="center" | geo
| align="center" | geo
| align="center" | 1.4.0, 3.1.0
| align="center" | 1.4.0, 3.1.0, 3.4.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ URL: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: https://github.com/NOAA-EMC/NCEPLIBS-g2/ URL: https://github.com/NOAA-EMC/NCEPLIBS-g2/ Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [http://hpc.pnl.gov/globalarrays/ ga]
| align="center" | [http://hpc.pnl.gov/globalarrays/ ga]
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| align="center" | [https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html gamess-us]
| align="center" | [https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html gamess-us]
| align="center" | chem
| align="center" | chem
| align="center" | 20210930-R2P1, 2020.2, 20170420-R1, 20180920-R3, 20190630-R1, 20220930-R2, 20230630-R1
| align="center" | 20210930-R2P1, 2020.2, 20170420-R1, 20180920-R3, 20190630-R1, 20220930-R2, 20230630-R1, 20230930-R2
| Documentation: [[GAMESS-US]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This version of GAMESS is built with Intel compilers and IntelMPI. It includes experimental MU CoupledCluster theory code. Homepage: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html URL: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Keyword:chem<br /><br /><br /></div>
| Documentation: [[GAMESS-US]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. This version of GAMESS-US is built with Intel compilers, mixed DDI, and OpenMPI 4.1. Homepage: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html URL: https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html Keyword:chem<br /><br /><br /></div>
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|-
| align="center" | [https://sourceforge.net/projects/soapdenovo2/files/GapCloser/ gapcloser]
| align="center" | [https://sourceforge.net/projects/soapdenovo2/files/GapCloser/ gapcloser]
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| align="center" | [http://www.broadinstitute.org/gatk/ gatk]
| align="center" | [http://www.broadinstitute.org/gatk/ gatk]
| align="center" | bio
| align="center" | bio
| align="center" | 3.7, 3.8, 4.0.0.0, 4.0.8.1, 4.0.12.0, 4.1.0.0, 4.1.2.0, 4.1.7.0, 4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0
| align="center" | 3.7, 3.8, 4.0.0.0, 4.0.8.1, 4.0.12.0, 4.1.0.0, 4.1.2.0, 4.1.7.0, 4.1.8.0, 4.1.8.1, 4.2.2.0, 4.2.4.0, 4.2.5.0, 4.4.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Homepage: http://www.broadinstitute.org/gatk/ URL: http://www.broadinstitute.org/gatk/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Homepage: http://www.broadinstitute.org/gatk/ URL: http://www.broadinstitute.org/gatk/ Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://gcc.gnu.org/ gcc]
| align="center" | [https://gcc.gnu.org/ gcc]
| align="center" | tools
| align="center" | tools
| align="center" | 4.8.5, 4.9.4, 5.4.0, 6.4.0, 7.3.0, 8.3.0, 8.4.0, 9.1.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0
| align="center" | 4.8.5, 4.9.4, 5.4.0, 6.4.0, 7.3.0, 8.3.0, 8.4.0, 9.1.0, 9.3.0, 10.2.0, 10.3.0, 11.3.0, 12.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). Homepage: https://gcc.gnu.org/ URL: https://gcc.gnu.org/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). Homepage: https://gcc.gnu.org/ URL: https://gcc.gnu.org/ Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://github.com/lstein/Perl-GD gd]
| align="center" | [https://github.com/lstein/Perl-GD gd]
| align="center" | -
| align="center" | -
| align="center" | 2.71
| align="center" | 2.71, 2.77
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GD.pm - Interface to Gd Graphics Library Homepage: https://github.com/lstein/Perl-GD URL: https://github.com/lstein/Perl-GD Extensions: ExtUtils::PkgConfig-1.16, GD-2.71<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GD.pm - Interface to Gd Graphics Library Homepage: https://github.com/lstein/Perl-GD URL: https://github.com/lstein/Perl-GD Extensions: ExtUtils::PkgConfig-1.16, GD-2.77<br /><br /><br /></div>
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|-
| align="center" | [http://www.gdal.org/ gdal]
| align="center" | [https://www.gdal.org/ gdal]
| align="center" | geo
| align="center" | geo
| align="center" | 2.1.3, 2.2.1, 2.4.1, 3.0.1, 3.0.4, 3.2.3, 3.4.1, 3.5.1
| align="center" | 2.1.3, 2.2.1, 2.4.1, 3.0.1, 3.0.4, 3.2.3, 3.4.1, 3.5.1, 3.7.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. Homepage: http://www.gdal.org/ URL: http://www.gdal.org/ Compatible modules: python/2.7.14 (default), python/3.5.4, python/3.6.3, python/3.7.4 Extensions: pygdal-3.0.1.5 Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. Homepage: https://www.gdal.org/ URL: https://www.gdal.org/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.10, python/3.10, python/3.11, python/3.11 Extensions: osgeo-3.7.2 Keyword:geo<br /><br /><br /></div>
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| align="center" | [https://sourceforge.net/projects/gdcm gdcm]
| align="center" | [https://sourceforge.net/projects/gdcm gdcm]
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| align="center" | [https://github.com/NVIDIA/gdrcopy gdrcopy]
| align="center" | [https://github.com/NVIDIA/gdrcopy gdrcopy]
| align="center" | -
| align="center" | -
| align="center" | 2.1, 2.3
| align="center" | 2.1, 2.3, 2.3.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy<br /><br /><br /></div>
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| align="center" | [http://geant4.cern.ch/ geant4]
| align="center" | [https://geant4.web.cern.ch/ geant4]
| align="center" | phys
| align="center" | phys
| align="center" | 9.6.p04, 10.02.p03, 10.04.p02, 10.06, 10.7.3, 11.1.0
| align="center" | 9.6.p04, 10.02.p03, 10.04.p02, 10.06, 10.7.3, 11.1.0, 11.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. Homepage: http://geant4.cern.ch/ URL: http://geant4.cern.ch/ Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. Homepage: https://geant4.web.cern.ch/ URL: https://geant4.web.cern.ch/ Keyword:phys<br /><br /><br /></div>
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| align="center" | [https://geant4.cern.ch/ geant4-data]
| align="center" | [https://geant4.cern.ch/ geant4-data]
| align="center" | -
| align="center" | -
| align="center" | 10.7.3, 11.1.0
| align="center" | 10.7.3, 11.1.0, 11.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Datasets for Geant4. Homepage: https://geant4.cern.ch/ URL: https://geant4.cern.ch/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Datasets for Geant4. Homepage: https://geant4.cern.ch/ URL: https://geant4.cern.ch/<br /><br /><br /></div>
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| align="center" | [http://veda.cs.uiuc.edu/Seq2Expr/ gemma]
| align="center" | [http://veda.cs.uiuc.edu/Seq2Expr/ gemma]
| align="center" | bio
| align="center" | bio
| align="center" | 0.97, 0.98.3
| align="center" | 0.97, 0.98.3, 0.98.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. Homepage: http://veda.cs.uiuc.edu/Seq2Expr/ URL: http://veda.cs.uiuc.edu/Seq2Expr/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. Homepage: http://veda.cs.uiuc.edu/Seq2Expr/ URL: http://veda.cs.uiuc.edu/Seq2Expr/ Keyword:bio<br /><br /><br /></div>
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GenMap - Fast and Exact Computation of Genome Mappability GenMap computes the uniqueness of k-mers for each position in the genome while allowing for up to e mismatches. More formally, the uniqueness or (k,e)-mappability can be described for every position as the reciprocal value of how often each k-mer occurs approximately in the genome, i.e., with up to e mismatches. Hence, a mappability value of 1 at position i indicates that the k-mer in the sequence at position i occurs only once in the sequence with up to e errors. A low mappability value indicates that this k-mer belongs to a repetitive region. GenMap can be applied to single or multiple genomes and helps finding regions that are unique or shared by many or all genomes. Homepage: https://github.com/cpockrandt/genmap URL: https://github.com/cpockrandt/genmap<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GenMap - Fast and Exact Computation of Genome Mappability GenMap computes the uniqueness of k-mers for each position in the genome while allowing for up to e mismatches. More formally, the uniqueness or (k,e)-mappability can be described for every position as the reciprocal value of how often each k-mer occurs approximately in the genome, i.e., with up to e mismatches. Hence, a mappability value of 1 at position i indicates that the k-mer in the sequence at position i occurs only once in the sequence with up to e errors. A low mappability value indicates that this k-mer belongs to a repetitive region. GenMap can be applied to single or multiple genomes and helps finding regions that are unique or shared by many or all genomes. Homepage: https://github.com/cpockrandt/genmap URL: https://github.com/cpockrandt/genmap<br /><br /><br /></div>
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| align="center" | [https://github.com/genometools/genometools genometools]
| align="center" | [http://genometools.org genometools]
| align="center" | bio
| align="center" | bio
| align="center" | 1.5.10, 1.6.1
| align="center" | 1.5.10, 1.6.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named libgenometools which contains a wide variety of classes for efficient and convenient implementation of sequence and annotation processing software. Homepage: https://github.com/genometools/genometools Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A comprehensive software library for efficient processing of structured genome annotations. Homepage: http://genometools.org URL: http://genometools.org Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://www.geopsy.org/ geopsy]
| align="center" | [https://www.geopsy.org/ geopsy]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geopsy team is developing, distributing and maintaining open source software for geophysical research and applications. Born during SESAME European Project, it has provided tools for processing ambient vibrations with site characterization in mind since 2005. Progressively, more conventional techniques (such as MASW or refraction) are included to offer a high quality, comprehensive and free platform for the interpretation of geophysical experiments. Homepage: https://www.geopsy.org/ URL: https://www.geopsy.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geopsy team is developing, distributing and maintaining open source software for geophysical research and applications. Born during SESAME European Project, it has provided tools for processing ambient vibrations with site characterization in mind since 2005. Progressively, more conventional techniques (such as MASW or refraction) are included to offer a high quality, comprehensive and free platform for the interpretation of geophysical experiments. Homepage: https://www.geopsy.org/ URL: https://www.geopsy.org/<br /><br /><br /></div>
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| align="center" | [http://trac.osgeo.org/geos geos]
| align="center" | [https://trac.osgeo.org/geos geos]
| align="center" | geo
| align="center" | geo
| align="center" | 3.6.1, 3.7.2, 3.7.3, 3.8.1, 3.9.1, 3.10.2
| align="center" | 3.6.1, 3.7.2, 3.7.3, 3.8.1, 3.9.1, 3.10.2, 3.12.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) Homepage: http://trac.osgeo.org/geos URL: http://trac.osgeo.org/geos Compatible modules: python/2.7.14 (default), python/3.5.4, python/3.6.3, python/3.7.4 Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) Homepage: https://trac.osgeo.org/geos URL: https://trac.osgeo.org/geos Keyword:geo<br /><br /><br /></div>
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| align="center" | [http://gfs.sourceforge.net/wiki/index.php/Main_Page gerris]
| align="center" | [http://gfs.sourceforge.net/wiki/index.php/Main_Page gerris]
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| align="center" | [http://git-annex.branchable.com/ git-annex]
| align="center" | [http://git-annex.branchable.com/ git-annex]
| align="center" | tools
| align="center" | tools
| align="center" | 6.20180807, 8.20200810, 10.20221003
| align="center" | 6.20180807, 8.20200810, 10.20221003, 10.20231129
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space. Homepage: http://git-annex.branchable.com/ URL: http://git-annex.branchable.com/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: git-annex allows managing files with git, without checking the file contents into git. While that may seem paradoxical, it is useful when dealing with files larger than git can currently easily handle, whether due to limitations in memory, time, or disk space. Homepage: http://git-annex.branchable.com/ URL: http://git-annex.branchable.com/ Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://git-lfs.github.com git-lfs]
| align="center" | [https://git-lfs.github.com git-lfs]
| align="center" | -
| align="center" | -
| align="center" | 2.11.0, 3.3.0
| align="center" | 2.11.0, 3.3.0, 3.4.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com Homepage: https://git-lfs.github.com URL: https://git-lfs.github.com<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com Homepage: https://git-lfs.github.com URL: https://git-lfs.github.com<br /><br /><br /></div>
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| align="center" | [http://glew.sourceforge.net/ glew]
| align="center" | [http://glew.sourceforge.net/ glew]
| align="center" | -
| align="center" | -
| align="center" | 2.1.0
| align="center" | 2.1.0, 2.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. Homepage: http://glew.sourceforge.net/ URL: http://glew.sourceforge.net/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. Homepage: http://glew.sourceforge.net/ URL: http://glew.sourceforge.net/<br /><br /><br /></div>
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| align="center" | [https://gmsh.info/ gmsh]
| align="center" | [https://gmsh.info/ gmsh]
| align="center" | phys
| align="center" | phys
| align="center" | 3.0.6, 4.0.7, 4.7.0, 4.10.5, 4.11.1
| align="center" | 3.0.6, 4.0.7, 4.7.0, 4.10.5, 4.11.1, 4.12.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Homepage: https://gmsh.info/ URL: https://gmsh.info/ Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Homepage: https://gmsh.info/ URL: https://gmsh.info/ Keyword:phys<br /><br /><br /></div>
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| align="center" | [http://gmt.soest.hawaii.edu/ gmt]
| align="center" | [https://www.generic-mapping-tools.org/ gmt]
| align="center" | geo
| align="center" | geo
| align="center" | 5.4.2, 6.2.0
| align="center" | 5.4.2, 6.2.0, 6.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. Homepage: http://gmt.soest.hawaii.edu/ URL: http://gmt.soest.hawaii.edu/ Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. Homepage: https://www.generic-mapping-tools.org/ URL: https://www.generic-mapping-tools.org/ Keyword:geo<br /><br /><br /></div>
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| align="center" | [http://melodi.ee.washington.edu/ gmtk]
| align="center" | [http://melodi.ee.washington.edu/ gmtk]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: gnina (pronounced NEE-na) is a molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks. It is a fork of smina, which is a fork of AutoDock Vina. Homepage: https://github.com/gnina/gnina URL: https://github.com/gnina/gnina<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: gnina (pronounced NEE-na) is a molecular docking program with integrated support for scoring and optimizing ligands using convolutional neural networks. It is a fork of smina, which is a fork of AutoDock Vina. Homepage: https://github.com/gnina/gnina URL: https://github.com/gnina/gnina<br /><br /><br /></div>
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| align="center" | [https://gnuplot.sourceforge.net/ gnuplot]
| align="center" | [http://gnuplot.sourceforge.net gnuplot]
| align="center" | vis
| align="center" | vis
| align="center" | 5.2.5, 5.2.8, 5.4.2, 5.4.6
| align="center" | 5.2.5, 5.2.8, 5.4.2, 5.4.6, 5.4.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Portable interactive, function plotting utility Homepage: https://gnuplot.sourceforge.net/ URL: https://gnuplot.sourceforge.net/ Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net URL: http://gnuplot.sourceforge.net Keyword:vis<br /><br /><br /></div>
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| align="center" | [https://www.golang.org go]
| align="center" | [https://www.golang.org go]
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| align="center" | [https://github.com/google/benchmark googlebenchmark]
| align="center" | [https://github.com/google/benchmark googlebenchmark]
| align="center" | -
| align="center" | -
| align="center" | 1.7.1
| align="center" | 1.7.1, 1.8.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google's library to benchmark code snippets, similar to unit tests. Homepage: https://github.com/google/benchmark URL: https://github.com/google/benchmark<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google's library to benchmark code snippets, similar to unit tests. Homepage: https://github.com/google/benchmark URL: https://github.com/google/benchmark<br /><br /><br /></div>
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| align="center" | [https://github.com/google/googletest googletest]
| align="center" | [https://github.com/google/googletest googletest]
| align="center" | tools
| align="center" | tools
| align="center" | 1.8.0, 1.10.0, 1.13.0
| align="center" | 1.8.0, 1.10.0, 1.13.0, 1.14.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Welcome to Google Test, Google-s C++ test framework! Please see the project page for more information as well as the mailing list for questions, discussions, and development. There is also an IRC channel on OFTC. Getting started information for Google Test is available in the Google Test Primer documentation. Google Mock is an extension to Google Test for writing and using C++ mock classes. See the separate Google Mock documentation. More detailed documentation for googletest (including build instructions) are in its interior googletest/README.md file. Homepage: https://github.com/google/googletest URL: https://github.com/google/googletest Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google's framework for writing C++ tests on a variety of platforms Homepage: https://github.com/google/googletest URL: https://github.com/google/googletest Keyword:tools<br /><br /><br /></div>
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|-
| align="center" | [https://github.com/data61/gossamer gossamer]
| align="center" | [https://github.com/data61/gossamer gossamer]
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| align="center" | vis
| align="center" | vis
| align="center" | 5.99.0
| align="center" | 5.99.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace URL: http://freecode.com/projects/grace Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. Homepage: http://freecode.com/projects/grace Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [http://grackle.readthedocs.io grackle]
| align="center" | [http://grackle.readthedocs.io grackle]
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| align="center" | -
| align="center" | -
| align="center" | 2.37, 2.45, 2.56
| align="center" | 2.37, 2.45, 2.56
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library. Homepage: https://graph-tool.skewed.de/ URL: https://graph-tool.skewed.de/ Compatible modules: python/3.8, python/3.9, python/3.10<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library. Homepage: https://graph-tool.skewed.de/ URL: https://graph-tool.skewed.de/ Compatible modules: python/3.9, python/3.10<br /><br /><br /></div>
|-
|-
| align="center" | [https://grass.osgeo.org/download/software/sources/ grass]
| align="center" | [https://grass.osgeo.org grass]
| align="center" | geo
| align="center" | geo
| align="center" | 7.4.0, 7.8.4, 8.2.1
| align="center" | 7.4.0, 7.8.4, 8.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GRASS: Geographic Resources Analysis Support System, commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/maps production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many governmental agencies and environmental consulting companies. Homepage: https://grass.osgeo.org/download/software/sources/ URL: https://grass.osgeo.org/download/software/sources/ Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization Homepage: https://grass.osgeo.org URL: https://grass.osgeo.org Keyword:geo<br /><br /><br /></div>
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|-
| align="center" | [https://software.ecmwf.int/wiki/display/GRIB/Home grib_api]
| align="center" | [https://software.ecmwf.int/wiki/display/GRIB/Home grib_api]
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| align="center" | [http://www.gromacs.org gromacs]
| align="center" | [http://www.gromacs.org gromacs]
| align="center" | chem
| align="center" | chem
| align="center" | 2018.3, 2018.6, 2018.7, 2019.1, 2019.3, 2019.6, 2020.2, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2
| align="center" | 2018.3, 2018.6, 2018.7, 2019.1, 2019.3, 2019.6, 2020.2, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2, 2023.3, 2024.1
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
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|-
| align="center" | [http://colvars.github.io/ gromacs-colvars]
| align="center" | [http://colvars.github.io/ gromacs-colvars]
| align="center" | chem
| align="center" | chem
| align="center" | 2020.6
| align="center" | 2020.6
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been patched with 'Colvars', a collective variables module for molecular simulation programs. This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://colvars.github.io/ URL: http://colvars.github.io/ Keyword:chem<br /><br /><br /></div>
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been patched with 'Colvars', a collective variables module for molecular simulation programs. This is a CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://colvars.github.io/ URL: http://colvars.github.io/ Keyword:chem<br /><br /><br /></div>
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| align="center" | [https://www.cp2k.org/tools:gromacs gromacs-cp2k]
| align="center" | [https://www.cp2k.org/tools:gromacs gromacs-cp2k]
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| align="center" | [https://www.hdfgroup.org/products/hdf4/ hdf]
| align="center" | [https://www.hdfgroup.org/products/hdf4/ hdf]
| align="center" | io
| align="center" | io
| align="center" | 4.2.12, 4.2.15
| align="center" | 4.2.12, 4.2.15, 4.2.16
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. Homepage: https://www.hdfgroup.org/products/hdf4/ URL: https://www.hdfgroup.org/products/hdf4/ Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. Homepage: https://www.hdfgroup.org/products/hdf4/ URL: https://www.hdfgroup.org/products/hdf4/ Keyword:io<br /><br /><br /></div>
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| align="center" | [https://portal.hdfgroup.org/display/support hdf5]
| align="center" | [https://portal.hdfgroup.org/display/support hdf5]
| align="center" | io
| align="center" | io
| align="center" | 1.8.18, 1.8.20, 1.8.21, 1.8.22, 1.10.1, 1.10.3, 1.10.5, 1.10.6, 1.10.7, 1.12.1, 1.12.2
| align="center" | 1.8.18, 1.8.20, 1.8.21, 1.8.22, 1.10.1, 1.10.3, 1.10.5, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: cached-property-1.5.2, h5py-3.6.0, numexpr-2.8.4, tables-3.7.0 Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11 Extensions: blosc2-2.2.9, cached-property-1.5.2, h5py-3.10.0, ndindex-1.7, numexpr-2.8.7, py-cpuinfo-9.0.0, tables-3.9.1 Keyword:io<br /><br /><br /></div>
|-
|-
| align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi]
| align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi]
| align="center" | io
| align="center" | io
| align="center" | 1.8.18, 1.10.3, 1.10.6, 1.10.7, 1.12.1, 1.12.2
| align="center" | 1.8.18, 1.10.3, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: cached-property-1.5.2, h5py-3.6.0, numexpr-2.8.4, tables-3.7.0 Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11 Extensions: blosc2-2.2.9, cached-property-1.5.2, h5py-3.10.0, ndindex-1.7, numexpr-2.8.7, py-cpuinfo-9.0.0, tables-3.9.1 Keyword:io<br /><br /><br /></div>
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|-
| align="center" | [https://support.hdfgroup.org/products/java/hdfview/ hdfview]
| align="center" | [https://support.hdfgroup.org/products/java/hdfview/ hdfview]
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| align="center" | [http://healpix.sourceforge.net/ healpix]
| align="center" | [http://healpix.sourceforge.net/ healpix]
| align="center" | -
| align="center" | -
| align="center" | 3.81
| align="center" | 3.81, 3.82
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Hierarchical Equal Area isoLatitude Pixelation of a sphere. Homepage: http://healpix.sourceforge.net/ URL: http://healpix.sourceforge.net/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Hierarchical Equal Area isoLatitude Pixelation of a sphere. Homepage: http://healpix.sourceforge.net/ URL: http://healpix.sourceforge.net/<br /><br /><br /></div>
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. Homepage: https://github.com/chhylp123/hifiasm URL: https://github.com/chhylp123/hifiasm<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. Homepage: https://github.com/chhylp123/hifiasm URL: https://github.com/chhylp123/hifiasm<br /><br /><br /></div>
|-
|-
| align="center" | [https://ccb.jhu.edu/software/hisat2/index.shtml hisat2]
| align="center" | [https://github.com/BlueBrain/HighFive highfive]
| align="center" | -
| align="center" | 2.9.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HighFive is a modern header-only C++11 friendly interface for libhdf5. Homepage: https://github.com/BlueBrain/HighFive URL: https://github.com/BlueBrain/HighFive<br /><br /><br /></div>
|-
| align="center" | [https://daehwankimlab.github.io/hisat2/ hisat2]
| align="center" | bio
| align="center" | bio
| align="center" | 2.1.0, 2.2.0, 2.2.1
| align="center" | 2.1.0, 2.2.0, 2.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml URL: https://ccb.jhu.edu/software/hisat2/index.shtml Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Homepage: https://daehwankimlab.github.io/hisat2/ URL: https://daehwankimlab.github.io/hisat2/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://hmmer.org/ hmmer]
| align="center" | [http://hmmer.org/ hmmer]
| align="center" | bio
| align="center" | bio
| align="center" | 3.1b2, 3.2.1, 3.3.2
| align="center" | 3.1b2, 3.2.1, 3.3.2, 3.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. Homepage: http://hmmer.org/ URL: http://hmmer.org/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. Homepage: http://hmmer.org/ URL: http://hmmer.org/ Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://www.htslib.org/ htslib]
| align="center" | [https://www.htslib.org/ htslib]
| align="center" | bio
| align="center" | bio
| align="center" | 1.9, 1.10.2, 1.11, 1.13, 1.14, 1.15.1, 1.16, 1.17
| align="center" | 1.9, 1.10.2, 1.11, 1.13, 1.14, 1.15.1, 1.16, 1.17, 1.18, 1.19
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [https://www.open-mpi.org/projects/hwloc/ hwloc]
| align="center" | [https://www.open-mpi.org/projects/hwloc/ hwloc]
| align="center" | -
| align="center" | -
| align="center" | 2.4.0, 2.7.1
| align="center" | 2.4.0, 2.7.1, 2.9.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. Homepage: https://www.open-mpi.org/projects/hwloc/ URL: https://www.open-mpi.org/projects/hwloc/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. Homepage: https://www.open-mpi.org/projects/hwloc/ URL: https://www.open-mpi.org/projects/hwloc/<br /><br /><br /></div>
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| align="center" | bio
| align="center" | bio
| align="center" | 2.3.14, 2.5.26, 2.5.49
| align="center" | 2.3.14, 2.5.26, 2.5.49
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HyPhy: Hypothesis testing using Phylogenies. HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R. Homepage: https://veg.github.io/hyphy-site/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning Homepage: https://veg.github.io/hyphy-site/ URL: https://veg.github.io/hyphy-site/ Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods hypre]
| align="center" | [https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods hypre]
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| align="center" | -
| align="center" | -
| align="center" | 1.1.3
| align="center" | 1.1.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. Homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ URL: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. Homepage: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/<br /><br /><br /></div>
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|-
| align="center" | [https://www.ncbi.nlm.nih.gov/igblast/intro.html igblast]
| align="center" | [https://www.ncbi.nlm.nih.gov/igblast/intro.html igblast]
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| align="center" | [https://igraph.org igraph]
| align="center" | [https://igraph.org igraph]
| align="center" | math
| align="center" | math
| align="center" | 0.7.1, 0.8.2, 0.9.10, 0.10.2
| align="center" | 0.7.1, 0.8.2, 0.9.10, 0.10.2, 0.10.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. Homepage: https://igraph.org URL: https://igraph.org Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11 Extensions: python-igraph-0.10.2 Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. Homepage: https://igraph.org URL: https://igraph.org Compatible modules: python/3.10, python/3.11 Extensions: python-igraph-0.11.2 Keyword:math<br /><br /><br /></div>
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|-
| align="center" | [https://www.broadinstitute.org/software/igv/ igv]
| align="center" | [https://www.broadinstitute.org/software/igv/ igv]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes Homepage: https://software.intel.com/en-us/articles/intel-mpi-benchmarks URL: https://software.intel.com/en-us/articles/intel-mpi-benchmarks<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes Homepage: https://software.intel.com/en-us/articles/intel-mpi-benchmarks URL: https://software.intel.com/en-us/articles/intel-mpi-benchmarks<br /><br /><br /></div>
|-
|-
| align="center" | [http://software.intel.com/en-us/intel-mkl/ imkl]
| align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html imkl]
| align="center" | math
| align="center" | math
| align="center" | 11.1.4.214, 11.3.4.258, 2017.1.132, 2017.4.239, 2018.1.163, 2018.3.222, 2019.2.187, 2019.3.199, 2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0
| align="center" | 11.1.4.214, 11.3.4.258, 2017.1.132, 2017.4.239, 2018.1.163, 2018.3.222, 2019.2.187, 2019.3.199, 2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0, 2023.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Homepage: http://software.intel.com/en-us/intel-mkl/ URL: http://software.intel.com/en-us/intel-mkl/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel oneAPI Math Kernel Library Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [http://software.intel.com/en-us/intel-mpi-library/ impi]
| align="center" | [http://software.intel.com/en-us/intel-mpi-library/ impi]
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| align="center" | bio
| align="center" | bio
| align="center" | 2.3.2
| align="center" | 2.3.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 Homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html URL: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 - Homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://jmarchini.org/software/#impute-5 impute5]
| align="center" | [https://jmarchini.org/software/#impute-5 impute5]
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| align="center" | [http://eddylab.org/infernal/ infernal]
| align="center" | [http://eddylab.org/infernal/ infernal]
| align="center" | bio
| align="center" | bio
| align="center" | 1.1.2, 1.1.3, 1.1.4
| align="center" | 1.1.2, 1.1.3, 1.1.4, 1.1.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Homepage: http://eddylab.org/infernal/ URL: http://eddylab.org/infernal/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. Homepage: http://eddylab.org/infernal/ URL: http://eddylab.org/infernal/ Keyword:bio<br /><br /><br /></div>
|-
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications Homepage: http://software.intel.com/en-us/intel-inspector-xe Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications Homepage: http://software.intel.com/en-us/intel-inspector-xe Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ intel]
| align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html intel]
| align="center" | tools
| align="center" | tools
| align="center" | 2014.6, 2016.4, 2017.1, 2017.5, 2018.3, 2019.3, 2020.1.217, 2021.2.0, 2022.1.0
| align="center" | 2014.6, 2016.4, 2017.1, 2017.5, 2018.3, 2019.3, 2020.1.217, 2021.2.0, 2022.1.0, 2023.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ URL: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel C, C++ and Fortran compilers (classic and oneAPI) Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html intel-opencl]
| align="center" | [https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html intel-opencl]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel's OpenCL CPU runtime Homepage: https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html URL: https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel's OpenCL CPU runtime Homepage: https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html URL: https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html<br /><br /><br /></div>
|-
|-
| align="center" | [http://software.intel.com/en-us/intel-mpi-library/ intelmpi]
| align="center" | [https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html intelmpi]
| align="center" | mpi
| align="center" | mpi
| align="center" | 2018.3.222, 2019.3.199, 2019.7.217, 2021.2.0
| align="center" | 2018.3.222, 2019.3.199, 2019.7.217, 2021.2.0, 2021.9.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel MPI Library, compatible with MPICH ABI. Note: like Open MPI, this module's mpicc calls the toolchain compiler. mpiicc calls icc, and mpigcc calls gcc, and similar for C++ and Fortran. Homepage: http://software.intel.com/en-us/intel-mpi-library/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel MPI Library, compatible with MPICH ABI Homepage: https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html URL: https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html<br /><br /><br /></div>
|-
|-
| align="center" | [https://intelxed.github.io/ intelxed]
| align="center" | [https://intelxed.github.io/ intelxed]
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| align="center" | [https://projects.coin-or.org/Ipopt ipopt]
| align="center" | [https://projects.coin-or.org/Ipopt ipopt]
| align="center" | -
| align="center" | -
| align="center" | 3.12.13, 3.14.11
| align="center" | 3.12.13, 3.14.11, 3.14.14
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization. Homepage: https://projects.coin-or.org/Ipopt URL: https://projects.coin-or.org/Ipopt<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization. Homepage: https://projects.coin-or.org/Ipopt URL: https://projects.coin-or.org/Ipopt<br /><br /><br /></div>
|-
|-
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| align="center" | -
| align="center" | -
| align="center" | 2020a, 2020b, 2021a, 2022a, 2023a, 2023b
| align="center" | 2020a, 2020b, 2021a, 2022a, 2023a, 2023b
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains ipykernel 2023a and its dependencies Homepage: https://ipython.org/ URL: https://ipython.org/ Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11 Extensions: asttokens-2.2.1, backcall-0.2.0, comm-0.1.2, debugpy-1.6.6, decorator-5.1.1, executing-1.2.0, importlib_metadata-5.2.0, ipykernel-6.21.2, ipython-8.10.0, ipython_genutils-0.2.0, jedi-0.18.2, jupyter_client-8.0.3, jupyter_core-5.2.0, matplotlib_inline-0.1.6, nest_asyncio-1.5.6, packaging-23.0, parso-0.8.3, pexpect-4.8.0, pickleshare-0.7.5, platformdirs-2.5.2, prompt_toolkit-3.0.37, psutil-5.9.4, ptyprocess-0.7.0, pure_eval-0.2.2, Pygments-2.14.0, python-dateutil-2.8.2, pyzmq-25.0.0, six-1.16.0, stack_data-0.6.2, tornado-6.2, traitlets-5.9.0, wcwidth-0.2.6, zipp-3.14.0<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains ipykernel 2023b and its dependencies Homepage: https://ipython.org/ URL: https://ipython.org/ Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: asttokens-2.2.1, backcall-0.2.0, comm-0.1.4, debugpy-1.6.7.post1, decorator-5.1.1, executing-1.2.0, importlib_metadata-6.8.0, ipykernel-6.25.1, ipython-8.15.0, ipython_genutils-0.2.0, jedi-0.19.0, jupyter_client-8.3.1, jupyter_core-5.3.1, matplotlib_inline-0.1.6, nest_asyncio-1.5.7, packaging-23.1, parso-0.8.3, pexpect-4.8.0, pickleshare-0.7.5, platformdirs-2.6.2, prompt_toolkit-3.0.39, psutil-5.9.5, ptyprocess-0.7.0, pure_eval-0.2.2, Pygments-2.16.1, python-dateutil-2.8.2, pyzmq-25.1.1, six-1.16.0, stack_data-0.6.2, tornado-6.3.3, traitlets-5.9.0, wcwidth-0.2.6, zipp-3.16.2<br /><br /><br /></div>
|-
|-
| align="center" | [https://ipython.org/ ipython-kernel]
| align="center" | [https://ipython.org/ ipython-kernel]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Interferometric synthetic aperture radar Scientific Computing Environment (ISCE) is a framework designed for the purpose of processing Interferometric Synthetic Aperture Radar (InSAR) data. The framework aspects of it have been designed as a general software development framework. It may have additional utility in a general sense for building other types of software packages. Homepage: https://github.com/isce-framework/isce2 URL: https://github.com/isce-framework/isce2<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Interferometric synthetic aperture radar Scientific Computing Environment (ISCE) is a framework designed for the purpose of processing Interferometric Synthetic Aperture Radar (InSAR) data. The framework aspects of it have been designed as a general software development framework. It may have additional utility in a general sense for building other types of software packages. Homepage: https://github.com/isce-framework/isce2 URL: https://github.com/isce-framework/isce2<br /><br /><br /></div>
|-
|-
| align="center" | [http://ispc.github.io/ ispc]
| align="center" | [https://ispc.github.io/ ispc]
| align="center" | -
| align="center" | -
| align="center" | 1.10.0, 1.13.0, 1.18.0
| align="center" | 1.10.0, 1.13.0, 1.18.0, 1.21.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware. Homepage: http://ispc.github.io/ , https://github.com/ispc/ispc/ URL: http://ispc.github.io/ , https://github.com/ispc/ispc/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware. Homepage: https://ispc.github.io/ , https://github.com/ispc/ispc/ URL: https://ispc.github.io/ , https://github.com/ispc/ispc/<br /><br /><br /></div>
|-
|-
| align="center" | [https://software.intel.com/en-us/intel-trace-analyzer/ itac]
| align="center" | [https://software.intel.com/en-us/intel-trace-analyzer/ itac]
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| align="center" | [https://itk.org itk]
| align="center" | [https://itk.org itk]
| align="center" | vis
| align="center" | vis
| align="center" | 4.13.1, 4.13.3, 5.0.1, 5.1.2, 5.2.1
| align="center" | 4.13.1, 4.13.3, 5.0.1, 5.1.2, 5.2.1, 5.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org URL: https://itk.org Compatible modules: python/3.10, python/3.9, python/3.8 Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org URL: https://itk.org Compatible modules: python/3.11, python/3.10 Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://github.com/andersen-lab/ivar ivar]
| align="center" | -
| align="center" | 1.4.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Homepage: https://github.com/andersen-lab/ivar URL: https://github.com/andersen-lab/ivar<br /><br /><br /></div>
|-
|-
| align="center" | [http://mcmc-jags.sourceforge.net/ jags]
| align="center" | [http://mcmc-jags.sourceforge.net/ jags]
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| align="center" | [https://www.ece.uvic.ca/~frodo/jasper/ jasper]
| align="center" | [https://www.ece.uvic.ca/~frodo/jasper/ jasper]
| align="center" | vis
| align="center" | vis
| align="center" | 1.900.1, 2.0.16
| align="center" | 1.900.1, 2.0.16, 4.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. Homepage: https://www.ece.uvic.ca/~frodo/jasper/ URL: https://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. Homepage: https://www.ece.uvic.ca/~frodo/jasper/ URL: https://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://openjdk.java.net java]
| align="center" | [http://openjdk.java.net java]
| align="center" | tools
| align="center" | tools
| align="center" | 1.7.0_80, 1.8.0_121, 1.8.0_192, 11.0.16_8, 11.0.2, 13.0.1, 13.0.2, 14.0.2, 17.0.2
| align="center" | 1.7.0_80, 1.8.0_121, 1.8.0_192, 1.8.0_292, 11.0.16_8, 11.0.22, 13.0.1, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1
| Documentation: [[Java]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: https://openjdk.java.net URL: https://openjdk.java.net Keyword:tools<br /><br /><br /></div>
| Documentation: [[Java]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://openjdk.java.net URL: http://openjdk.java.net Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.cl.cam.ac.uk/~mgk25/jbigkit/ jbigkit]
| align="center" | [https://www.cl.cam.ac.uk/~mgk25/jbigkit/ jbigkit]
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| align="center" | [https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html jsoncpp]
| align="center" | [https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html jsoncpp]
| align="center" | -
| align="center" | -
| align="center" | 1.9.4
| align="center" | 1.9.4, 1.9.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. Homepage: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html URL: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. Homepage: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html URL: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html<br /><br /><br /></div>
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|-
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| align="center" | [https://julialang.org julia]
| align="center" | [https://julialang.org julia]
| align="center" | tools
| align="center" | tools
| align="center" | 1.0.2, 1.1.0, 1.1.1, 1.2.0, 1.3.0, 1.4.0, 1.4.1, 1.5.2, 1.6.0, 1.6.1, 1.7.0, 1.8.1, 1.8.5, 1.9.1
| align="center" | 1.0.2, 1.1.0, 1.1.1, 1.2.0, 1.3.0, 1.4.0, 1.4.1, 1.5.2, 1.6.0, 1.6.1, 1.7.0, 1.8.1, 1.8.5, 1.9.1, 1.9.3, 1.10.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Julia is a high-level, high-performance dynamic programming language for numerical computing Homepage: https://julialang.org URL: https://julialang.org Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Julia is a high-level, high-performance dynamic programming language for numerical computing Homepage: https://julialang.org URL: https://julialang.org Keyword:tools<br /><br /><br /></div>
|-
|-
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| align="center" | [http://kaiju.binf.ku.dk/ kaiju]
| align="center" | [http://kaiju.binf.ku.dk/ kaiju]
| align="center" | bio
| align="center" | bio
| align="center" | 1.6.2, 1.7.4
| align="center" | 1.6.2, 1.7.4, 1.10.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments Homepage: http://kaiju.binf.ku.dk/ URL: http://kaiju.binf.ku.dk/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments Homepage: http://kaiju.binf.ku.dk/ URL: http://kaiju.binf.ku.dk/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://msa.cgb.ki.se/ kalign]
| align="center" | [https://github.com/TimoLassmann/kalign kalign]
| align="center" | -
| align="center" | -
| align="center" | 2.03
| align="center" | 2.03, 3.3.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A fast and accurate multiple sequence alignment algorithm. Homepage: http://msa.cgb.ki.se/ URL: http://msa.cgb.ki.se/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kalign is a fast multiple sequence alignment program for biological sequences. Homepage: https://github.com/TimoLassmann/kalign URL: https://github.com/TimoLassmann/kalign<br /><br /><br /></div>
|-
|-
| align="center" | [https://pachterlab.github.io/kallisto/ kallisto]
| align="center" | [https://pachterlab.github.io/kallisto/ kallisto]
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| align="center" | bio
| align="center" | bio
| align="center" | 401, 20180716
| align="center" | 401, 20180716
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kent utilities: collection of tools used by the UCSC genome browser. Homepage: http://genome.cse.ucsc.edu/ URL: http://genome.cse.ucsc.edu/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kent utilities: collection of tools used by the UCSC genome browser. Homepage: http://genome.cse.ucsc.edu/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://openkim.org/ kim]
| align="center" | [https://openkim.org/ kim]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. Homepage: https://github.com/marbl/Krona/wiki/KronaTools URL: https://github.com/marbl/Krona/wiki/KronaTools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. Homepage: https://github.com/marbl/Krona/wiki/KronaTools URL: https://github.com/marbl/Krona/wiki/KronaTools<br /><br /><br /></div>
|-
|-
| align="center" | [https://lammps.sandia.gov/ lammps-omp]
| align="center" | [https://www.lammps.org lammps-omp]
| align="center" | chem
| align="center" | chem
| align="center" | 20190807, 20201029, 20210929, 20220623
| align="center" | 20190807, 20201029, 20210929, 20220623, 20230802
| Documentation: [[LAMMPS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. Homepage: https://lammps.sandia.gov/ URL: https://lammps.sandia.gov/ Keyword:chem<br /><br /><br /></div>
| Documentation: [[LAMMPS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. Homepage: https://www.lammps.org URL: https://www.lammps.org Compatible modules: python/3.11, python/3.10 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [http://lammps.sandia.gov/ lammps-user-intel]
| align="center" | [http://lammps.sandia.gov/ lammps-user-intel]
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| align="center" | chem
| align="center" | chem
| align="center" | 1.2.1
| align="center" | 1.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open source density functional tight binding molecular dynamics. Homepage: https://github.com/lanl/LATTE URL: https://github.com/lanl/LATTE Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open source density functional tight binding molecular dynamics. Homepage: https://github.com/lanl/LATTE Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://wiki.dlang.org/LDC ldc]
| align="center" | [https://wiki.dlang.org/LDC ldc]
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| align="center" | 1.82.0
| align="center" | 1.82.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. Homepage: http://www.leptonica.org URL: http://www.leptonica.org<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. Homepage: http://www.leptonica.org URL: http://www.leptonica.org<br /><br /><br /></div>
|-
| align="center" | [https://github.com/Esri/lerc lerc]
| align="center" | -
| align="center" | 4.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds). Homepage: https://github.com/Esri/lerc URL: https://github.com/Esri/lerc<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/google/leveldb leveldb]
| align="center" | [https://github.com/google/leveldb leveldb]
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| align="center" | [https://jugit.fz-juelich.de/mlz/libcerf libcerf]
| align="center" | [https://jugit.fz-juelich.de/mlz/libcerf libcerf]
| align="center" | math
| align="center" | math
| align="center" | 1.5, 1.13, 1.17, 2.1
| align="center" | 1.5, 1.13, 1.17, 2.1, 2.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. Homepage: https://jugit.fz-juelich.de/mlz/libcerf URL: https://jugit.fz-juelich.de/mlz/libcerf Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. Homepage: https://jugit.fz-juelich.de/mlz/libcerf URL: https://jugit.fz-juelich.de/mlz/libcerf Keyword:math<br /><br /><br /></div>
|-
|-
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| align="center" | [https://www.opendap.org/software/libdap libdap]
| align="center" | [https://www.opendap.org/software/libdap libdap]
| align="center" | -
| align="center" | -
| align="center" | 3.20.6
| align="center" | 3.20.6, 3.20.11
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. Homepage: https://www.opendap.org/software/libdap URL: https://www.opendap.org/software/libdap<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. Homepage: https://www.opendap.org/software/libdap URL: https://www.opendap.org/software/libdap<br /><br /><br /></div>
|-
|-
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| align="center" | [https://ofiwg.github.io/libfabric/ libfabric]
| align="center" | [https://ofiwg.github.io/libfabric/ libfabric]
| align="center" | -
| align="center" | -
| align="center" | 1.10.1, 1.11.0, 1.12.1, 1.15.1
| align="center" | 1.10.1, 1.11.0, 1.12.1, 1.15.1, 1.18.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. Homepage: https://ofiwg.github.io/libfabric/ URL: https://ofiwg.github.io/libfabric/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. Homepage: https://ofiwg.github.io/libfabric/ URL: https://ofiwg.github.io/libfabric/<br /><br /><br /></div>
|-
| align="center" | [https://launchpad.net/libfdf libfdf]
| align="center" | -
| align="center" | 0.2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF). Homepage: https://launchpad.net/libfdf URL: https://launchpad.net/libfdf<br /><br /><br /></div>
|-
|-
| align="center" | [https://sourceware.org/libffi/ libffi]
| align="center" | [https://sourceware.org/libffi/ libffi]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. Homepage: https://sourceware.org/libffi/ URL: https://sourceware.org/libffi/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. Homepage: https://sourceware.org/libffi/ URL: https://sourceware.org/libffi/<br /><br /><br /></div>
|-
|-
| align="center" | [https://libgd.github.io/ libgd]
| align="center" | [https://libgd.github.io libgd]
| align="center" | vis
| align="center" | vis
| align="center" | 2.2.5, 2.3.0, 2.3.3
| align="center" | 2.2.5, 2.3.0, 2.3.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GD is an open source code library for the dynamic creation of images by programmers. Homepage: https://libgd.github.io/ URL: https://libgd.github.io/ Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GD is an open source code library for the dynamic creation of images by programmers. Homepage: https://libgd.github.io URL: https://libgd.github.io Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/HomerReid/libGDSII libgdsii]
| align="center" | [https://github.com/HomerReid/libGDSII libgdsii]
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| align="center" | bio
| align="center" | bio
| align="center" | 0.7
| align="center" | 0.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ URL: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/libharu/libharu/ libharu]
| align="center" | [http://libharu.org/ libharu]
| align="center" | -
| align="center" | -
| align="center" | 2.3.0
| align="center" | 2.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libHaru is a free, cross platform, open source library for generating PDF files. Homepage: https://github.com/libharu/libharu/ URL: https://github.com/libharu/libharu/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libHaru is a free, cross platform, open source library for generating PDF files. Homepage: http://libharu.org/ URL: http://libharu.org/<br /><br /><br /></div>
|-
|-
| align="center" | [https://sourceforge.net/p/libint/ libint]
| align="center" | [https://github.com/evaleev/libint libint]
| align="center" | chem
| align="center" | chem
| align="center" | 1.1.6, 2.0.3, 2.2.0, 2.4.2, 2.6.0
| align="center" | 1.1.6, 2.0.3, 2.2.0, 2.4.2, 2.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. Homepage: https://sourceforge.net/p/libint/ URL: https://sourceforge.net/p/libint/ Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. Homepage: https://github.com/evaleev/libint URL: https://github.com/evaleev/libint Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.gnu.org/software/libmatheval/ libmatheval]
| align="center" | [http://www.gnu.org/software/libmatheval/ libmatheval]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A small C and Python library for reading PLINK genotype files. Homepage: https://github.com/mfranberg/libplinkio Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A small C and Python library for reading PLINK genotype files. Homepage: https://github.com/mfranberg/libplinkio Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://launchpad.net/libpsml libpsml]
| align="center" | [https://gitlab.com/siesta-project/libraries/libpsml libpsml]
| align="center" | -
| align="center" | -
| align="center" | 1.1.8
| align="center" | 1.1.8, 1.1.12
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Language (PSML) format. Homepage: https://launchpad.net/libpsml URL: https://launchpad.net/libpsml<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A library to handle pseudopotentials in PSML format Homepage: https://gitlab.com/siesta-project/libraries/libpsml URL: https://gitlab.com/siesta-project/libraries/libpsml<br /><br /><br /></div>
|-
|-
| align="center" | [http://libqglviewer.com/ libqglviewer]
| align="center" | [http://libqglviewer.com/ libqglviewer]
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| align="center" | -
| align="center" | -
| align="center" | 1.1.0
| align="center" | 1.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores. Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo<br /><br /><br /></div>
|-
|-
| align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9]
| align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Homepage: https://doc.libsodium.org/ URL: https://doc.libsodium.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Homepage: https://doc.libsodium.org/ URL: https://doc.libsodium.org/<br /><br /><br /></div>
|-
|-
| align="center" | [http://libspatialindex.github.io libspatialindex]
| align="center" | [https://libspatialindex.org libspatialindex]
| align="center" | phys
| align="center" | phys
| align="center" | 1.8.5
| align="center" | 1.8.5, 1.9.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API Homepage: http://libspatialindex.github.io URL: http://libspatialindex.github.io Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API Homepage: https://libspatialindex.org URL: https://libspatialindex.org Keyword:phys<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.gaia-gis.it/fossil/libspatialite/home libspatialite]
| align="center" | [https://www.gaia-gis.it/fossil/libspatialite/home libspatialite]
| align="center" | phys
| align="center" | phys
| align="center" | 4.3.0a, 5.0.1
| align="center" | 4.3.0a, 5.0.1, 5.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. Homepage: https://www.gaia-gis.it/fossil/libspatialite/home URL: https://www.gaia-gis.it/fossil/libspatialite/home Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. Homepage: https://www.gaia-gis.it/fossil/libspatialite/home URL: https://www.gaia-gis.it/fossil/libspatialite/home Keyword:phys<br /><br /><br /></div>
|-
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: liburing provides helpers to setup and teardown io_uring instances, and also a simplified interface for applications that don't need (or want) to deal with the full kernel side implementation. Homepage: https://github.com/axboe/liburing URL: https://github.com/axboe/liburing<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: liburing provides helpers to setup and teardown io_uring instances, and also a simplified interface for applications that don't need (or want) to deal with the full kernel side implementation. Homepage: https://github.com/axboe/liburing URL: https://github.com/axboe/liburing<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxc]
| align="center" | [https://libxc.gitlab.io libxc]
| align="center" | chem
| align="center" | chem
| align="center" | 2.2.2, 3.0.0, 3.0.1, 4.2.1, 4.2.3, 4.3.4, 5.0.0, 5.1.3, 5.2.3
| align="center" | 2.2.2, 3.0.0, 3.0.1, 4.2.1, 4.2.3, 4.3.4, 5.0.0, 5.1.3, 5.2.3, 6.2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc URL: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: https://libxc.gitlab.io URL: https://libxc.gitlab.io Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [http://xmlsoft.org/ libxslt]
| align="center" | [http://xmlsoft.org/ libxslt]
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| align="center" | 1.8.2, 1.16.1
| align="center" | 1.8.2, 1.16.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). Homepage: https://github.com/hfp/libxsmm URL: https://github.com/hfp/libxsmm Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). Homepage: https://github.com/hfp/libxsmm URL: https://github.com/hfp/libxsmm Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://pyyaml.org/wiki/LibYAML libyaml]
| align="center" | -
| align="center" | 0.2.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LibYAML is a YAML parser and emitter written in C. Homepage: https://pyyaml.org/wiki/LibYAML URL: https://pyyaml.org/wiki/LibYAML<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/limix/liknorm liknorm]
| align="center" | [https://github.com/limix/liknorm liknorm]
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| align="center" | [https://llvm.org/ llvm]
| align="center" | [https://llvm.org/ llvm]
| align="center" | tools
| align="center" | tools
| align="center" | 6.0.1, 7.0.0, 8.0.1, 9.0.1, 13.0.1, 14.0.3
| align="center" | 6.0.1, 7.0.0, 8.0.1, 9.0.1, 13.0.1, 14.0.3, 16.0.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. Homepage: https://llvm.org/ URL: https://llvm.org/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. Homepage: https://llvm.org/ URL: https://llvm.org/ Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://symas.com/lmdb lmdb]
| align="center" | [https://symas.com/lmdb lmdb]
| align="center" | -
| align="center" | -
| align="center" | 0.9.24
| align="center" | 0.9.24, 0.9.31
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. Homepage: https://symas.com/lmdb URL: https://symas.com/lmdb<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. Homepage: https://symas.com/lmdb URL: https://symas.com/lmdb<br /><br /><br /></div>
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| align="center" | math
| align="center" | math
| align="center" | 5.5.2.5
| align="center" | 5.5.2.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/ URL: https://sourceforge.net/projects/lpsolve/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/ Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.lstc.com/products/ls-opt ls-opt]
| align="center" | [http://www.lstc.com/products/ls-opt ls-opt]
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| align="center" | [https://github.com/tothuhien/lsd2 lsd2]
| align="center" | [https://github.com/tothuhien/lsd2 lsd2]
| align="center" | -
| align="center" | -
| align="center" | 1.9.7, 2.3
| align="center" | 1.9.7, 2.3, 2.4.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Least-squares methods to estimate rates and dates from phylogenies Homepage: https://github.com/tothuhien/lsd2 URL: https://github.com/tothuhien/lsd2<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Least-squares methods to estimate rates and dates from phylogenies Homepage: https://github.com/tothuhien/lsd2 URL: https://github.com/tothuhien/lsd2<br /><br /><br /></div>
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| align="center" | bio
| align="center" | bio
| align="center" | 0.2.13
| align="center" | 0.2.13
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A probabilistic framework for structural variant discovery. Homepage: https://github.com/arq5x/lumpy-sv URL: https://github.com/arq5x/lumpy-sv Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A probabilistic framework for structural variant discovery. Homepage: https://github.com/arq5x/lumpy-sv Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/Macaulay2/M2 m2]
| align="center" | [https://github.com/Macaulay2/M2 m2]
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| align="center" | [https://icl.cs.utk.edu/magma/ magma]
| align="center" | [https://icl.cs.utk.edu/magma/ magma]
| align="center" | math
| align="center" | math
| align="center" | 2.4.0, 2.5.0, 2.5.4, 2.6.1, 2.7.1
| align="center" | 2.4.0, 2.5.0, 2.5.4, 2.6.1, 2.7.1, 2.7.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. Homepage: https://icl.cs.utk.edu/magma/ URL: https://icl.cs.utk.edu/magma/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. Homepage: https://icl.cs.utk.edu/magma/ URL: https://icl.cs.utk.edu/magma/ Keyword:math<br /><br /><br /></div>
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|-
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| align="center" | bio
| align="center" | bio
| align="center" | 1.2.2, 1.6.0
| align="center" | 1.2.2, 1.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. The method is designed for rapid analysis on standard compute hardware: NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a 20 core server, and most WGS tumor/normal analyses can be completed within 2 hours. Manta combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. It provides scoring models for germline variants in small sets of diploid samples and somatic variants in matched tumor/normal sample pairs. There is experimental support for analysis of unmatched tumor samples as well. Manta accepts input read mappings from BAM or CRAM files and reports all SV and indel inferences in VCF 4.1 format. See the user guide for a full description of capabilities and limitations. Homepage: https://github.com/Illumina/manta Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. Homepage: https://github.com/Illumina/manta URL: https://github.com/Illumina/manta Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [https://github.com/UCSC-nanopore-cgl/MarginPolish marginpolish]
| align="center" | [https://github.com/UCSC-nanopore-cgl/MarginPolish marginpolish]
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| align="center" | [https://docs.computecanada.ca/wiki/Database_servers. mariadb]
| align="center" | [https://docs.computecanada.ca/wiki/Database_servers. mariadb]
| align="center" | tools
| align="center" | tools
| align="center" | 10.1.21, 10.4.11, 10.4.13, 10.6.12
| align="center" | 10.1.21, 10.4.11, 10.4.13, 10.6.12, 11.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MariaDB An enhanced, drop-in replacement for MySQL For more information please take a look at https://docs.computecanada.ca/wiki/Database_servers. Homepage: https://mariadb.org/ URL: https://mariadb.org/ Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Extensions: DBD::mysql-4.050, Devel::CheckLib-1.13, IO::CaptureOutput-1.1104, mysql-connector-python-8.0.21, PyMySQL-0.10.0 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MariaDB An enhanced, drop-in replacement for MySQL For more information please take a look at https://docs.computecanada.ca/wiki/Database_servers. Homepage: https://mariadb.org/ URL: https://mariadb.org/ Compatible modules: Extensions: DBD::mysql-5.004, Devel::CheckLib-1.16, IO::CaptureOutput-1.1105, mysql-connector-python-8.2.0, PyMySQL-1.1.0 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://downloads.mariadb.org/connector-c/ mariadb-connector-c]
| align="center" | [https://downloads.mariadb.org/connector-c/ mariadb-connector-c]
| align="center" | -
| align="center" | -
| align="center" | 3.1.7
| align="center" | 3.1.7, 3.3.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. Homepage: https://downloads.mariadb.org/connector-c/ URL: https://downloads.mariadb.org/connector-c/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. Homepage: https://downloads.mariadb.org/connector-c/ URL: https://downloads.mariadb.org/connector-c/<br /><br /><br /></div>
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| align="center" | [https://sourceforge.net/projects/matio/ matio]
| align="center" | [https://sourceforge.net/projects/matio/ matio]
| align="center" | io
| align="center" | io
| align="center" | 1.5.2, 1.5.19
| align="center" | 1.5.19, 1.5.26
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: matio is an C library for reading and writing Matlab MAT files. Homepage: https://sourceforge.net/projects/matio/ URL: https://sourceforge.net/projects/matio/ Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: matio is an C library for reading and writing Matlab MAT files. Homepage: https://sourceforge.net/projects/matio/ URL: https://sourceforge.net/projects/matio/ Keyword:io<br /><br /><br /></div>
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|-
| align="center" | [https://www.mathworks.com/products/matlab matlab]
| align="center" | [http://www.mathworks.com/products/matlab matlab]
| align="center" | tools
| align="center" | tools
| align="center" | 2014a, 2016b, 2017a, 2018a, 2018b, 2019a, 2019b, 2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3
| align="center" | 2014a, 2016b, 2017a, 2018a, 2018b, 2019a, 2019b, 2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3, 2023b.2
| Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: https://www.mathworks.com/products/matlab URL: https://www.mathworks.com/products/matlab Keyword:tools<br /><br /><br /></div>
| Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab URL: http://www.mathworks.com/products/matlab Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://maven.apache.org/index.html maven]
| align="center" | [https://maven.apache.org/index.html maven]
| align="center" | tools
| align="center" | tools
| align="center" | 3.5.0, 3.6.3
| align="center" | 3.5.0, 3.6.3, 3.9.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. Homepage: https://maven.apache.org/index.html URL: https://maven.apache.org/index.html Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. Homepage: https://maven.apache.org/index.html URL: https://maven.apache.org/index.html Keyword:tools<br /><br /><br /></div>
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| align="center" | math
| align="center" | math
| align="center" | 14.137
| align="center" | 14.137
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ URL: http://micans.org/mcl/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ Keyword:math<br /><br /><br /></div>
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|-
| align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr]
| align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr]
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| align="center" | bio
| align="center" | bio
| align="center" | 1.2.7, 1.2.9
| align="center" | 1.2.7, 1.2.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. Homepage: https://github.com/voutcn/megahit URL: https://github.com/voutcn/megahit Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Homepage: https://github.com/voutcn/megahit URL: https://github.com/voutcn/megahit Compatible modules: Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [http://meme-suite.org meme]
| align="center" | [http://meme-suite.org meme]
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| align="center" | math
| align="center" | math
| align="center" | 2.3.0
| align="center" | 2.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mesh-Quality Improvement Library Homepage: https://software.sandia.gov/mesquite/ URL: https://software.sandia.gov/mesquite/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mesh-Quality Improvement Library Homepage: https://software.sandia.gov/mesquite/ Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [https://dtcenter.org/met/users/support/online_tutorial/METv6.1/index.php met]
| align="center" | [https://dtcenter.org/ met]
| align="center" | phys
| align="center" | phys
| align="center" | 8.0_bugfix, 9.0.2, 9.1.1
| align="center" | 8.0_bugfix, 9.0.2, 9.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Model Evaluation Tools (MET) is a highly configurable, state-of-the-art suite of verification tools designed for the verification and evaluation of numerical weather forecasts. Although MET was developed at the Developmental Testbed Center (DTC) to be used with the Weather Research and Forecasting (WRF) modeling system, the data formats and standards used allow MET to be run on the output of other modeling systems as well. Homepage: ihttps://dtcenter.org/met/users/support/online_tutorial/METv6.1/index.php URL: ihttps://dtcenter.org/met/users/support/online_tutorial/METv6.1/index.php Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Model Evaluation Tools (MET) is a highly configurable, state-of-the-art suite of verification tools designed for the verification and evaluation of numerical weather forecasts. Although MET was developed at the Developmental Testbed Center (DTC) to be used with the Weather Research and Forecasting (WRF) modeling system, the data formats and standards used allow MET to be run on the output of other modeling systems as well. Homepage: https://dtcenter.org/ URL: https://dtcenter.org/ Keyword:phys<br /><br /><br /></div>
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| align="center" | [https://docs.computecanada.ca/wiki/META_package_for_serial_farming meta-farm]
| align="center" | [https://docs.computecanada.ca/wiki/META_package_for_serial_farming meta-farm]
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| align="center" | [https://bitbucket.org/berkeleylab/metabat metabat]
| align="center" | [https://bitbucket.org/berkeleylab/metabat metabat]
| align="center" | bio
| align="center" | bio
| align="center" | 2.12.1, 2.14
| align="center" | 2.12.1, 2.14, 2.17
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An efficient tool for accurately reconstructing single genomes from complex microbial communities Homepage: https://bitbucket.org/berkeleylab/metabat URL: https://bitbucket.org/berkeleylab/metabat Compatible modules: Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An efficient tool for accurately reconstructing single genomes from complex microbial communities Homepage: https://bitbucket.org/berkeleylab/metabat URL: https://bitbucket.org/berkeleylab/metabat Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [https://metaeuk.soedinglab.org metaeuk]
| align="center" | [https://metaeuk.soedinglab.org metaeuk]
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| align="center" | bio
| align="center" | bio
| align="center" | 2011-03-25
| align="center" | 2011-03-25
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats. Availability and implementation: METAL, including source code, documentation, examples, and executables, is available at: http://www.sph.umich.edu/csg/abecasis/metal/ If you use Metal please fill out the registration form on the page: http://csg.sph.umich.edu/abecasis/metal/download/ Contact: goncalo@umich.edu Homepage: http://www.sph.umich.edu/csg/abecasis/metal/ URL: http://www.sph.umich.edu/csg/abecasis/metal/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: METAL provides a computationally efficient tool for meta-analysis of genome-wide association scans, which is a commonly used approach for improving power complex traits gene mapping studies. METAL provides a rich scripting interface and implements efficient memory management to allow analyses of very large data sets and to support a variety of input file formats. Availability and implementation: METAL, including source code, documentation, examples, and executables, is available at: http://www.sph.umich.edu/csg/abecasis/metal/ If you use Metal please fill out the registration form on the page: http://csg.sph.umich.edu/abecasis/metal/download/ Contact: goncalo@umich.edu Homepage: http://www.sph.umich.edu/csg/abecasis/metal/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/DiltheyLab/MetaMaps metamaps]
| align="center" | [https://github.com/DiltheyLab/MetaMaps metamaps]
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| align="center" | [http://bic-mni.github.io/ minc-toolkit]
| align="center" | [http://bic-mni.github.io/ minc-toolkit]
| align="center" | bio
| align="center" | bio
| align="center" | 1.9.16, 1.9.18.1
| align="center" | 1.9.16, 1.9.18.1, 1.9.18.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Medical Imaging NetCDF Toolkit Homepage: http://bic-mni.github.io/ URL: http://bic-mni.github.io/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Medical Imaging NetCDF Toolkit Homepage: http://bic-mni.github.io/ URL: http://bic-mni.github.io/ Keyword:bio<br /><br /><br /></div>
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GATB - The Genome Analysis Toolbox with de-Bruijn graph. Homepage: https://github.com/GATB/gatb-core URL: https://github.com/GATB/gatb-core Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GATB - The Genome Analysis Toolbox with de-Bruijn graph. Homepage: https://github.com/GATB/gatb-core URL: https://github.com/GATB/gatb-core Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [https://github.com/lh3/miniasm miniasm]
| align="center" | [https://github.com/lh3/minimap2 miniasm]
| align="center" | bio
| align="center" | bio
| align="center" | 0.3
| align="center" | 0.3-20191007
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ultrafast de novo assembly for long noisy reads (though having no consensus step). Homepage: https://github.com/lh3/miniasm Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads. Homepage: https://github.com/lh3/minimap2 URL: https://github.com/lh3/minimap2 Keyword:bio<br /><br /><br /></div>
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|-
| align="center" | [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]
| align="center" | [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]
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| align="center" | [https://github.com/lh3/minimap2 minimap2]
| align="center" | [https://github.com/lh3/minimap2 minimap2]
| align="center" | bio
| align="center" | bio
| align="center" | 2.13, 2.17, 2.18, 2.24
| align="center" | 2.13, 2.17, 2.18, 2.24, 2.26, 2.28
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. Homepage: https://github.com/lh3/minimap2 URL: https://github.com/lh3/minimap2 Compatible modules: python/3.7, python/3.8, python/3.9 Extensions: mappy-2.18 Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. Homepage: https://github.com/lh3/minimap2 URL: https://github.com/lh3/minimap2 Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://omics.informatics.indiana.edu/MinPath minpath]
| align="center" | [https://omics.informatics.indiana.edu/MinPath minpath]
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| align="center" | [https://mmseqs.com mmseqs2]
| align="center" | [https://mmseqs.com mmseqs2]
| align="center" | -
| align="center" | -
| align="center" | 10-6d92c, 14-7e284, 13-45111
| align="center" | 10-6d92c, 14-7e284, 15-6f452, 13-45111
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com<br /><br /><br /></div>
|-
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPFI, a multiple precision interval arithmetic library based on MPFR MPFI stands for Multiple Precision Floating-point Interval library. Homepage: http://perso.ens-lyon.fr/nathalie.revol/software.html Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPFI, a multiple precision interval arithmetic library based on MPFR MPFI stands for Multiple Precision Floating-point Interval library. Homepage: http://perso.ens-lyon.fr/nathalie.revol/software.html Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [https://bitbucket.org/mpi4py/mpi4py mpi4py]
| align="center" | [https://github.com/mpi4py/mpi4py mpi4py]
| align="center" | tools
| align="center" | tools
| align="center" | 3.0.0, 3.0.3, 3.1.2, 3.1.3, 3.1.4
| align="center" | 3.0.0, 3.0.3, 3.1.2, 3.1.3, 3.1.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. Homepage: https://bitbucket.org/mpi4py/mpi4py URL: https://bitbucket.org/mpi4py/mpi4py Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. Homepage: https://github.com/mpi4py/mpi4py URL: https://github.com/mpi4py/mpi4py Compatible modules: python/3.10, python/3.11 Extensions: mpi4py-3.1.4 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.mpich.org/ mpich]
| align="center" | [http://www.mpich.org/ mpich]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPSolve is a C package to solve polynomials and secular equations. It released under the terms of the GNU General public license as it specified in the COPYING file inside the source directory. Homepage: https://numpi.dm.unipi.it/software/mpsolve URL: https://numpi.dm.unipi.it/software/mpsolve<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPSolve is a C package to solve polynomials and secular equations. It released under the terms of the GNU General public license as it specified in the COPYING file inside the source directory. Homepage: https://numpi.dm.unipi.it/software/mpsolve URL: https://numpi.dm.unipi.it/software/mpsolve<br /><br /><br /></div>
|-
|-
| align="center" | [https://nbisweden.github.io/MrBayes/ mrbayes]
| align="center" | [http://mrbayes.csit.fsu.edu mrbayes]
| align="center" | bio
| align="center" | bio
| align="center" | 3.2.6, 3.2.7a
| align="center" | 3.2.6, 3.2.7a
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. Homepage: https://nbisweden.github.io/MrBayes/ URL: https://nbisweden.github.io/MrBayes/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MrBayes is a program for the Bayesian estimation of phylogeny. Homepage: http://mrbayes.csit.fsu.edu URL: http://mrbayes.csit.fsu.edu Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.brain.org.au/software/index.html#mrtrix mrtrix]
| align="center" | [http://www.brain.org.au/software/index.html#mrtrix mrtrix]
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| align="center" | chem
| align="center" | chem
| align="center" | 1.7.3.1
| align="center" | 1.7.3.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Multiscale Coarse-Graining (MS-CG) method is a variational force-matching technique developed by the Voth group. This project serves as the workhorse implementation of the method used as a standard force-matching code. The development of MS-CG is supported by academic research grants. If you use this package, please cite at least one of these papers: - S. Izvekov and G. A. Voth, J. Chem. Phys. 123, 134105 (2005). - W. G. Noid, et al., J. Chem. Phys. 128, 244114 (2008). - W. G. Noid et al., J. Chem. Phys. 128, 244115 (2008). - L. Lu, S. Izvekov, A. Das, H. C. Andersen, and G. A. Voth, Journal of Chemical Theory and Computation, 6(3), 954-965 (2010). Homepage: https://github.com/uchicago-voth/MSCG-release URL: https://github.com/uchicago-voth/MSCG-release Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Multiscale Coarse-Graining (MS-CG) method is a variational force-matching technique developed by the Voth group. This project serves as the workhorse implementation of the method used as a standard force-matching code. The development of MS-CG is supported by academic research grants. If you use this package, please cite at least one of these papers: - S. Izvekov and G. A. Voth, J. Chem. Phys. 123, 134105 (2005). - W. G. Noid, et al., J. Chem. Phys. 128, 244114 (2008). - W. G. Noid et al., J. Chem. Phys. 128, 244115 (2008). - L. Lu, S. Izvekov, A. Das, H. C. Andersen, and G. A. Voth, Journal of Chemical Theory and Computation, 6(3), 954-965 (2010). Homepage: https://github.com/uchicago-voth/MSCG-release Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/stschiff/msmc msmc]
| align="center" | [https://github.com/stschiff/msmc msmc]
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| align="center" | [https://mujoco.org/ mujoco]
| align="center" | [https://mujoco.org/ mujoco]
| align="center" | -
| align="center" | -
| align="center" | 2.2.0, 2.2.2, 2.3.6
| align="center" | 2.2.0, 2.2.2, 2.3.6, 3.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and development in robotics, biomechanics, graphics and animation, machine learning, and other areas which demand fast and accurate simulation of articulated structures interacting with their environment. Homepage: https://mujoco.org/ URL: https://mujoco.org/ Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: absl-py-1.2.0, mujoco-2.3.6, PyOpenGL-3.1.6<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and development in robotics, biomechanics, graphics and animation, machine learning, and other areas which demand fast and accurate simulation of articulated structures interacting with their environment. Homepage: https://mujoco.org/ URL: https://mujoco.org/ Compatible modules: python/3.10, python/3.11 Extensions: mujoco-3.0.1<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/ekg/multichoose multichoose]
| align="center" | [https://github.com/ekg/multichoose multichoose]
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| align="center" | bio
| align="center" | bio
| align="center" | 3.23, 4.0.0beta2
| align="center" | 3.23, 4.0.0beta2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/ URL: http://mummer.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://graal.ens-lyon.fr/MUMPS/ mumps-metis]
| align="center" | [https://graal.ens-lyon.fr/MUMPS/ mumps-metis]
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| align="center" | [http://www.mysql.com/ mysql]
| align="center" | [http://www.mysql.com/ mysql]
| align="center" | tools
| align="center" | tools
| align="center" | 5.7.36
| align="center" | 5.7.36, 8.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MySQL is one of the world's most widely used open-source relational database management system (RDBMS). Homepage: http://www.mysql.com/ URL: http://www.mysql.com/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MySQL is one of the world's most widely used open-source relational database management system (RDBMS). Homepage: http://www.mysql.com/ URL: http://www.mysql.com/ Keyword:tools<br /><br /><br /></div>
|-
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| align="center" | [https://developer.nvidia.com/nccl nccl]
| align="center" | [https://developer.nvidia.com/nccl nccl]
| align="center" | tools
| align="center" | tools
| align="center" | 2.3.5, 2.4.2, 2.5.6, 2.7.8, 2.8.4, 2.11.4, 2.12.12, 2.18.5
| align="center" | 2.3.5, 2.4.2, 2.5.6, 2.7.8, 2.8.4, 2.11.4, 2.12.12, 2.18.3, 2.18.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. Homepage: https://developer.nvidia.com/nccl URL: https://developer.nvidia.com/nccl Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. Homepage: https://developer.nvidia.com/nccl URL: https://developer.nvidia.com/nccl Keyword:tools<br /><br /><br /></div>
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient. Homepage: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html URL: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient. Homepage: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html URL: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.ncl.ucar.edu ncl]
| align="center" | [http://www.ncl.ucar.edu ncl]
| align="center" | vis
| align="center" | vis
| align="center" | 6.6.2
| align="center" | 6.6.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization. Homepage: https://www.ncl.ucar.edu URL: https://www.ncl.ucar.edu Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NCL is an interpreted language designed specifically for scientific data analysis and visualization. Homepage: http://www.ncl.ucar.edu URL: http://www.ncl.ucar.edu Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://nco.sourceforge.net nco]
| align="center" | [https://nco.sourceforge.net nco]
| align="center" | io
| align="center" | io
| align="center" | 4.6.6, 4.9.5, 5.0.6
| align="center" | 4.6.6, 4.9.5, 5.0.6, 5.1.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 Homepage: https://nco.sourceforge.net URL: https://nco.sourceforge.net Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 Homepage: https://nco.sourceforge.net URL: https://nco.sourceforge.net Keyword:io<br /><br /><br /></div>
|-
|-
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| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf]
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf]
| align="center" | io
| align="center" | io
| align="center" | 4.6.1, 4.7.0, 4.7.3, 4.7.4, 4.8.0, 4.9.0
| align="center" | 4.6.1, 4.7.0, 4.7.3, 4.7.4, 4.8.0, 4.9.0, 4.9.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Compatible modules: python/3.9, python/3.9, python/3.10, python/3.10, python/3.9, python/3.9, python/3.10, python/3.10 Extensions: cftime-1.6.2, netCDF4-1.6.1 Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.10, python/3.10, python/3.11, python/3.11 Extensions: certifi-2023.7.22, cftime-1.6.2, netCDF4-1.6.4 Keyword:io<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++]
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++]
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| align="center" | io
| align="center" | io
| align="center" | 4.2
| align="center" | 4.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ URL: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-c++4]
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-c++4]
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| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran]
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran]
| align="center" | io
| align="center" | io
| align="center" | 4.4.4, 4.4.5, 4.5.2, 4.5.3, 4.6.0
| align="center" | 4.4.4, 4.4.5, 4.5.2, 4.5.3, 4.6.0, 4.6.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran-mpi]
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran-mpi]
| align="center" | io
| align="center" | io
| align="center" | 4.4.4, 4.5.1, 4.5.2, 4.5.3, 4.6.0
| align="center" | 4.4.4, 4.5.1, 4.5.2, 4.5.3, 4.6.0, 4.6.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-mpi]
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-mpi]
| align="center" | io
| align="center" | io
| align="center" | 4.4.1.1, 4.6.1, 4.7.4, 4.8.0, 4.8.1, 4.9.0
| align="center" | 4.4.1.1, 4.6.1, 4.7.4, 4.8.0, 4.8.1, 4.9.0, 4.9.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Compatible modules: python/3.8, python/3.8, python/3.9, python/3.9, python/3.10, python/3.10, python/3.8, python/3.8, python/3.9, python/3.9, python/3.10, python/3.10 Extensions: netCDF4-1.5.8 Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/ URL: https://www.unidata.ucar.edu/software/netcdf/ Compatible modules: python/3.10, python/3.10, python/3.11, python/3.11, python/3.10, python/3.10, python/3.11, python/3.11 Extensions: certifi-2023.7.22, cftime-1.6.2, netCDF4-1.6.4 Keyword:io<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.lysator.liu.se/~nisse/nettle/ nettle]
| align="center" | [http://www.lysator.liu.se/~nisse/nettle/ nettle]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. Homepage: http://www.lysator.liu.se/~nisse/nettle/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. Homepage: http://www.lysator.liu.se/~nisse/nettle/<br /><br /><br /></div>
|-
|-
| align="center" | [https://pypi.python.org/pypi/networkx networkx]
| align="center" | [http://python.org/ networkx]
| align="center" | tools
| align="center" | tools
| align="center" | 1.1, 2.1
| align="center" | 1.1, 2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Homepage: https://pypi.python.org/pypi/networkx Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains networkx for different Python versions Homepage: http://python.org/ Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.neuron.yale.edu/neuron neuron]
| align="center" | [http://www.neuron.yale.edu/neuron neuron]
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| align="center" | [https://www.nextflow.io/ nextflow]
| align="center" | [https://www.nextflow.io/ nextflow]
| align="center" | -
| align="center" | -
| align="center" | 19.04.0, 19.10.0, 20.04.1, 20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3
| align="center" | 19.04.0, 19.10.0, 20.04.1, 20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3, 23.10.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Homepage: https://www.nextflow.io/ URL: https://www.nextflow.io/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Homepage: https://www.nextflow.io/ URL: https://www.nextflow.io/<br /><br /><br /></div>
|-
|-
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| align="center" | math
| align="center" | math
| align="center" | 2.4.2, 2.6.1, 2.6.2, 2.7.0, 2.7.1
| align="center" | 2.4.2, 2.6.1, 2.6.2, 2.7.0, 2.7.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3.6, python/3.6, python/3.7, python/3.7, python/3.8, python/3.8, python/3.6, python/3.6, python/3.7, python/3.7, python/3.8, python/3.8 Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [https://nodejs.org nodejs]
| align="center" | [https://nodejs.org nodejs]
| align="center" | tools
| align="center" | tools
| align="center" | 11.1.0, 12.16.1, 14.4.0, 15.2.1
| align="center" | 11.1.0, 12.16.1, 14.4.0, 15.2.1, 18.17.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Node.js is a platform built on Chrome's V8 JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. Homepage: https://nodejs.org URL: https://nodejs.org Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. Homepage: https://nodejs.org URL: https://nodejs.org Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR nspr]
| align="center" | [https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR nspr]
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| align="center" | [https://developer.nvidia.com/hpc-sdk/ nvhpc]
| align="center" | [https://developer.nvidia.com/hpc-sdk/ nvhpc]
| align="center" | tools
| align="center" | tools
| align="center" | 20.7, 22.1, 22.7, 23.7
| align="center" | 20.7, 22.1, 22.7, 23.7, 23.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) Homepage: https://developer.nvidia.com/hpc-sdk/ URL: https://developer.nvidia.com/hpc-sdk/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) Homepage: https://developer.nvidia.com/hpc-sdk/ URL: https://developer.nvidia.com/hpc-sdk/<br /><br /><br /></div>
|-
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A collection of tools for use with nvptx-none GCC toolchains: https://gcc.gnu.org/wiki/nvptx Homepage: https://github.com/MentorEmbedded/nvptx-tools URL: https://github.com/MentorEmbedded/nvptx-tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A collection of tools for use with nvptx-none GCC toolchains: https://gcc.gnu.org/wiki/nvptx Homepage: https://github.com/MentorEmbedded/nvptx-tools URL: https://github.com/MentorEmbedded/nvptx-tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.nwchem-sw.org nwchem]
| align="center" | [http://www.nwchem-sw.org nwchem]
| align="center" | chem
| align="center" | chem
| align="center" | 6.6.revision27746, 7.0.2-p1, 6.8.1
| align="center" | 6.6.revision27746, 7.0.2-p1, 6.8.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. Homepage: https://www.nwchem-sw.org URL: https://www.nwchem-sw.org Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. Homepage: http://www.nwchem-sw.org URL: http://www.nwchem-sw.org Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/dzerbino/oases oases]
| align="center" | [https://github.com/dzerbino/oases oases]
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| align="center" | [https://www.opencascade.com/ occt]
| align="center" | [https://www.opencascade.com/ occt]
| align="center" | -
| align="center" | -
| align="center" | 7.4.0
| align="center" | 7.4.0, 7.7.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. Homepage: https://www.opencascade.com/ URL: https://www.opencascade.com/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. Homepage: https://www.opencascade.com/ URL: https://www.opencascade.com/<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.gnu.org/software/octave/ octave]
| align="center" | [https://www.gnu.org/software/octave/ octave]
| align="center" | tools
| align="center" | tools
| align="center" | 4.2.2, 5.2.0
| align="center" | 4.2.2, 5.2.0, 7.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Homepage: http://www.gnu.org/software/octave/ URL: http://www.gnu.org/software/octave/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GNU Octave is a high-level interpreted language, primarily intended for numerical computations. Homepage: https://www.gnu.org/software/octave/ URL: https://www.gnu.org/software/octave/ Extensions: control-3.5.0, general-2.1.3, io-2.6.4, optim-1.6.2, signal-1.4.5, statistics-1.4.3, struct-1.0.18 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page octopus]
| align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page octopus]
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| align="center" | chem
| align="center" | chem
| align="center" | 2.4.1, 3.0.0, 3.1.1
| align="center" | 2.4.1, 3.0.0, 3.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.6, python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://openbabel.org openbabel-omp]
| align="center" | [https://openbabel.org openbabel-omp]
| align="center" | chem
| align="center" | chem
| align="center" | 3.1.1
| align="center" | 3.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.6, python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://xianyi.github.com/OpenBLAS/ openblas]
| align="center" | [http://www.openblas.net/ openblas]
| align="center" | math
| align="center" | math
| align="center" | 0.2.20, 0.3.4, 0.3.6, 0.3.9, 0.3.17, 0.3.18, 0.3.20
| align="center" | 0.2.20, 0.3.4, 0.3.6, 0.3.9, 0.3.17, 0.3.18, 0.3.20, 0.3.24
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: https://xianyi.github.com/OpenBLAS/ URL: https://xianyi.github.com/OpenBLAS/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://www.openblas.net/ URL: http://www.openblas.net/ Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [http://xianyi.github.com/OpenBLAS/ openblas-64bits]
| align="center" | [http://xianyi.github.com/OpenBLAS/ openblas-64bits]
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| align="center" | [http://opencolorio.org/ opencolorio]
| align="center" | [http://opencolorio.org/ opencolorio]
| align="center" | vis
| align="center" | vis
| align="center" | 1.0.9, 1.1.1, 2.2.1
| align="center" | 1.0.9, 1.1.1, 2.2.1, 2.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. Homepage: http://opencolorio.org/ URL: http://opencolorio.org/ Compatible modules: python/3.10, python/3.9, python/3.8 Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. Homepage: http://opencolorio.org/ URL: http://opencolorio.org/ Compatible modules: python/3.11, python/3.10 Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [http://opencv.org/ opencv]
| align="center" | [http://opencv.org/ opencv]
| align="center" | vis
| align="center" | vis
| align="center" | 3.4.3, 4.1.0, 4.2.0, 4.4.0, 4.5.1, 4.5.5, 4.6.0, 4.7.0, 4.8.0
| align="center" | 3.4.3, 4.1.0, 4.2.0, 4.4.0, 4.5.1, 4.5.5, 4.6.0, 4.7.0, 4.8.0, 4.8.1, 4.9.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ URL: http://opencv.org/ Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4 Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Homepage: http://opencv.org/ URL: http://opencv.org/ Compatible modules: python/3.10, python/3.11 Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [http://opencv.org/ opencv_contrib]
| align="center" | [http://opencv.org/ opencv_contrib]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenFAST is a multi-physics, multi-fidelity tool for simulating the coupled dynamic response of wind turbines. Practically speaking, OpenFAST is the framework (or glue code) that couples computational modules for aerodynamics, hydrodynamics for offshore structures, control and electrical system (servo) dynamics, and structural dynamics to enable coupled nonlinear aero-hydro-servo-elastic simulation in the time domain. OpenFAST enables the analysis of a range of wind turbine configurations, including two- or three-blade horizontal-axis rotor, pitch or stall regulation, rigid or teetering hub, upwind or downwind rotor, and lattice or tubular tower. The wind turbine can be modeled on land or offshore on fixed-bottom or floating substructures. Homepage: https://openfast.readthedocs.io/en/main/index.html URL: https://openfast.readthedocs.io/en/main/index.html<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenFAST is a multi-physics, multi-fidelity tool for simulating the coupled dynamic response of wind turbines. Practically speaking, OpenFAST is the framework (or glue code) that couples computational modules for aerodynamics, hydrodynamics for offshore structures, control and electrical system (servo) dynamics, and structural dynamics to enable coupled nonlinear aero-hydro-servo-elastic simulation in the time domain. OpenFAST enables the analysis of a range of wind turbine configurations, including two- or three-blade horizontal-axis rotor, pitch or stall regulation, rigid or teetering hub, upwind or downwind rotor, and lattice or tubular tower. The wind turbine can be modeled on land or offshore on fixed-bottom or floating substructures. Homepage: https://openfast.readthedocs.io/en/main/index.html URL: https://openfast.readthedocs.io/en/main/index.html<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.openfoam.org/ openfoam]
| align="center" | [https://www.openfoam.com/ openfoam]
| align="center" | phys
| align="center" | phys
| align="center" | 2.2.2, 2.3.1, 3.0.1, 4.1, 5.0, 6.20180813, 7, 9, 10, v1712, v1812, v1906, v1912, v2006, v2012, v2112, v2206, v2212, v2306
| align="center" | 2.2.2, 2.3.1, 3.0.1, 4.1, 5.0, 6.20180813, 7, 9, 10, v1712, v1812, v1906, v1912, v2006, v2012, v2112, v2206, v2212, v2306
| Documentation: [[OpenFOAM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: https://www.openfoam.org/ URL: https://www.openfoam.org/ Keyword:phys<br /><br /><br /></div>
| Documentation: [[OpenFOAM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: https://www.openfoam.com/ URL: https://www.openfoam.com/ Keyword:phys<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.extend-project.de/ openfoam-extend]
| align="center" | [http://www.extend-project.de/ openfoam-extend]
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| align="center" | [https://github.com/OpenImageDenoise/oidn openimagedenoise]
| align="center" | [https://github.com/OpenImageDenoise/oidn openimagedenoise]
| align="center" | -
| align="center" | -
| align="center" | 1.2.2, 1.4.3
| align="center" | 1.2.2, 1.4.3, 2.0.1, 2.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Open Image Denoise is an open source library of high-performance, high-quality denoising filters for images rendered with ray tracing. Homepage: https://github.com/OpenImageDenoise/oidn URL: https://github.com/OpenImageDenoise/oidn<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Open Image Denoise is an open source library of high-performance, high-quality denoising filters for images rendered with ray tracing. Homepage: https://github.com/OpenImageDenoise/oidn URL: https://github.com/OpenImageDenoise/oidn<br /><br /><br /></div>
|-
|-
| align="center" | [https://openimageio.org/ openimageio]
| align="center" | [https://openimageio.org/ openimageio]
| align="center" | vis
| align="center" | vis
| align="center" | 1.8.15, 2.1.17.0, 2.4.7.1
| align="center" | 1.8.15, 2.1.17.0, 2.4.7.1, 2.4.14.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. Homepage: https://openimageio.org/ URL: https://openimageio.org/ Compatible modules: python/3.10, python/3.9, python/3.8 Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. Homepage: https://openimageio.org/ URL: https://openimageio.org/ Compatible modules: python/3.10, python/3.11 Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://docs.openmc.org/en/stable/ openmc]
| align="center" | [https://docs.openmc.org/en/stable/ openmc]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMC is a community-developed Monte Carlo neutron and photon transport simulation code. It is capable of performing fixed source, k-eigenvalue, and subcritical multiplication calculations on models built using either a constructive solid geometry or CAD representation. OpenMC supports both continuous-energy and multigroup transport. The continuous-energy particle interaction data is based on a native HDF5 format that can be generated from ACE files produced by NJOY. Parallelism is enabled via a hybrid MPI and OpenMP programming model. Homepage: https://docs.openmc.org/en/stable/ URL: https://docs.openmc.org/en/stable/ Compatible modules: python/3.9, python/3.10, python/3.11<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMC is a community-developed Monte Carlo neutron and photon transport simulation code. It is capable of performing fixed source, k-eigenvalue, and subcritical multiplication calculations on models built using either a constructive solid geometry or CAD representation. OpenMC supports both continuous-energy and multigroup transport. The continuous-energy particle interaction data is based on a native HDF5 format that can be generated from ACE files produced by NJOY. Parallelism is enabled via a hybrid MPI and OpenMP programming model. Homepage: https://docs.openmc.org/en/stable/ URL: https://docs.openmc.org/en/stable/ Compatible modules: python/3.9, python/3.10, python/3.11<br /><br /><br /></div>
|-
|-
| align="center" | [https://simtk.org/home/openmm openmm]
| align="center" | [http://openmm.org openmm]
| align="center" | chem
| align="center" | chem
| align="center" | 7.1.1, 7.4.1, 7.5.0, 7.6.0, 7.7.0, 8.0.0
| align="center" | 7.1.1, 7.4.1, 7.5.0, 7.6.0, 7.7.0, 8.0.0
| Documentation: [[OpenMM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. - CC-Wiki: OpenMM Homepage: https://simtk.org/home/openmm URL: https://simtk.org/home/openmm Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4 Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3.10, python/3.11 Extensions: pdbfixer-1.8.1 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [http://openmm.org openmm-alphafold]
| align="center" | [http://openmm.org openmm-alphafold]
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| align="center" | chem
| align="center" | chem
| align="center" | 18.9, 20.07, 20.10
| align="center" | 18.9, 20.07, 20.10
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMolcas is a quantum chemistry software package. The key feature of OpenMolcas is the multiconfigurational approach to the electronic structure. This module does include WFA and GRID-IT and EFP but does NOT include DMRG and NECI modules. Homepage: https://gitlab.com/Molcas/OpenMolcas URL: https://gitlab.com/Molcas/OpenMolcas Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMolcas is a quantum chemistry software package Homepage: https://gitlab.com/Molcas/OpenMolcas URL: https://gitlab.com/Molcas/OpenMolcas Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.open-mpi.org/ openmpi]
| align="center" | [https://www.open-mpi.org/ openmpi]
| align="center" | mpi
| align="center" | mpi
| align="center" | 1.8.8, 1.10.7, 2.1.1, 3.1.2, 3.1.4, 4.0.1, 4.0.3, 4.0.5, 4.1.1, 4.1.4
| align="center" | 1.8.8, 1.10.7, 2.1.1, 3.1.2, 3.1.4, 4.0.1, 4.0.3, 4.0.5, 4.1.1, 4.1.4, 4.1.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-3 implementation. Homepage: https://www.open-mpi.org/ URL: https://www.open-mpi.org/ Keyword:mpi<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Open MPI Project is an open source MPI-3 implementation. Homepage: https://www.open-mpi.org/ URL: https://www.open-mpi.org/ Keyword:mpi<br /><br /><br /></div>
|-
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/ Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/ Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://code.google.com/p/openpgm/ openpgm]
| align="center" | [http://code.google.com/p/openpgm/ openpgm]
| align="center" | tools
| align="center" | tools
| align="center" | 5.2.122
| align="center" | 5.2.122
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. Homepage: https://code.google.com/p/openpgm/ URL: https://code.google.com/p/openpgm/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. Homepage: http://code.google.com/p/openpgm/ Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/OpenRefine/OpenRefine openrefine]
| align="center" | [https://github.com/OpenRefine/OpenRefine openrefine]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. This version is built using DISTRIBUTED_MP platform setting. Homepage: http://opensees.berkeley.edu/ URL: http://opensees.berkeley.edu/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. This version is built using DISTRIBUTED_MP platform setting. Homepage: http://opensees.berkeley.edu/ URL: http://opensees.berkeley.edu/<br /><br /><br /></div>
|-
|-
| align="center" | [http://openslide.org/ openslide]
| align="center" | [https://github.com/openslide/openslide openslide]
| align="center" | vis
| align="center" | vis
| align="center" | 3.4.1
| align="center" | 3.4.1, 4.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). Homepage: http://openslide.org/ URL: http://openslide.org/ Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C library for reading virtual slide images Homepage: https://github.com/openslide/openslide URL: https://github.com/openslide/openslide Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/PixarAnimationStudios/OpenSubdiv opensubdiv]
| align="center" | [https://github.com/PixarAnimationStudios/OpenSubdiv opensubdiv]
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| align="center" | [https://github.com/AcademySoftwareFoundation/openvdb openvdb]
| align="center" | [https://github.com/AcademySoftwareFoundation/openvdb openvdb]
| align="center" | -
| align="center" | -
| align="center" | 7.0.0, 10.0.1
| align="center" | 7.0.0, 10.0.1, 10.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenVDB is an open source C++ library comprising a novel hierarchical data structure and a large suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production. Homepage: https://github.com/AcademySoftwareFoundation/openvdb URL: https://github.com/AcademySoftwareFoundation/openvdb<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenVDB is an open source C++ library comprising a novel hierarchical data structure and a large suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production. Homepage: https://github.com/AcademySoftwareFoundation/openvdb URL: https://github.com/AcademySoftwareFoundation/openvdb<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/OpenVKL/openvkl openvkl]
| align="center" | [https://github.com/OpenVKL/openvkl openvkl]
| align="center" | -
| align="center" | -
| align="center" | 0.10.0, 1.3.1
| align="center" | 0.10.0, 1.3.1, 1.3.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Open Volume Kernel Library (Intel Open VKL) is a collection of high-performance volume computation kernels, developed at Intel. The target users of Open VKL are graphics application engineers who want to improve the performance of their volume rendering applications by leveraging Open VKLs performance-optimized kernels, which include volume traversal and sampling functionality for a variety of volumetric data formats. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Homepage: https://github.com/OpenVKL/openvkl URL: https://github.com/OpenVKL/openvkl<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Open Volume Kernel Library (Intel Open VKL) is a collection of high-performance volume computation kernels, developed at Intel. The target users of Open VKL are graphics application engineers who want to improve the performance of their volume rendering applications by leveraging Open VKLs performance-optimized kernels, which include volume traversal and sampling functionality for a variety of volumetric data formats. The kernels are optimized for the latest Intel processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Homepage: https://github.com/OpenVKL/openvkl URL: https://github.com/OpenVKL/openvkl<br /><br /><br /></div>
|-
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| align="center" | [https://developer.nvidia.com/optix optix]
| align="center" | [https://developer.nvidia.com/optix optix]
| align="center" | -
| align="center" | -
| align="center" | 6.5.0, 7.7.0
| align="center" | 6.5.0, 7.7.0, 8.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPUs massive ray tracing power using state-of-the-art GPU algorithms. Homepage: https://developer.nvidia.com/optix URL: https://developer.nvidia.com/optix<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPUs massive ray tracing power using state-of-the-art GPU algorithms. Homepage: https://developer.nvidia.com/optix URL: https://developer.nvidia.com/optix<br /><br /><br /></div>
|-
| align="center" | [https://support.illumina.com/downloads/dragen_decompression_software_v261_software-linux.html orad]
| align="center" | -
| align="center" | 2.6.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://support.illumina.com/downloads/dragen_decompression_software_v261_software-linux.html URL: https://support.illumina.com/downloads/dragen_decompression_software_v261_software-linux.html<br /><br /><br /></div>
|-
|-
| align="center" | [http://cec.mpg.de/forum/ orca]
| align="center" | [http://cec.mpg.de/forum/ orca]
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| align="center" | bio
| align="center" | bio
| align="center" | 2.0.9
| align="center" | 2.0.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/ Extensions: DBD::mysql-4.050, Devel::CheckLib-1.13, IO::CaptureOutput-1.1104, Mock::Config-0.03 Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/ospray/ospray ospray]
| align="center" | [https://github.com/ospray/ospray ospray]
| align="center" | -
| align="center" | -
| align="center" | 1.8.5, 2.2.0, 2.10.0
| align="center" | 1.8.5, 2.2.0, 2.10.0, 2.12.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel OSPRay is an open source, scalable, and portable ray tracing engine for high-performance, high-fidelity visualization on Intel Architecture CPUs. Homepage: https://github.com/ospray/ospray URL: https://github.com/ospray/ospray<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel OSPRay is an open source, scalable, and portable ray tracing engine for high-performance, high-fidelity visualization on Intel Architecture CPUs. Homepage: https://github.com/ospray/ospray URL: https://github.com/ospray/ospray<br /><br /><br /></div>
|-
|-
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| align="center" | [https://mvapich.cse.ohio-state.edu/benchmarks/ osu-micro-benchmarks]
| align="center" | [https://mvapich.cse.ohio-state.edu/benchmarks/ osu-micro-benchmarks]
| align="center" | tools
| align="center" | tools
| align="center" | 5.3.2, 5.6.1, 5.6.2, 5.6.3, 5.9
| align="center" | 5.3.2, 5.6.1, 5.6.2, 5.6.3, 5.9, 7.1-1, 7.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OSU Micro-Benchmarks Homepage: https://mvapich.cse.ohio-state.edu/benchmarks/ URL: https://mvapich.cse.ohio-state.edu/benchmarks/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OSU Micro-Benchmarks Homepage: https://mvapich.cse.ohio-state.edu/benchmarks/ URL: https://mvapich.cse.ohio-state.edu/benchmarks/ Keyword:tools<br /><br /><br /></div>
|-
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| align="center" | [http://abacus.gene.ucl.ac.uk/software/paml.html paml]
| align="center" | [http://abacus.gene.ucl.ac.uk/software/paml.html paml]
| align="center" | bio
| align="center" | bio
| align="center" | 4.9h, 4.9j
| align="center" | 4.9h, 4.9j, 4.10.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html URL: http://abacus.gene.ucl.ac.uk/software/paml.html Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html URL: http://abacus.gene.ucl.ac.uk/software/paml.html Keyword:bio<br /><br /><br /></div>
|-
|-
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| align="center" | [https://www.paraview.org paraview]
| align="center" | [https://www.paraview.org paraview]
| align="center" | vis
| align="center" | vis
| align="center" | 5.5.2, 5.8.0, 5.9.1, 5.10.0, 5.11.0
| align="center" | 5.5.2, 5.8.0, 5.9.1, 5.10.0, 5.11.0, 5.11.2
| Documentation: [[Visualization]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:vis<br /><br /><br /></div>
| Documentation: [[Visualization]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: https://www.paraview.org URL: https://www.paraview.org Compatible modules: python/3.10, python/3.11 Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.paraview.org paraview-offscreen]
| align="center" | [https://www.paraview.org paraview-offscreen]
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| align="center" | math
| align="center" | math
| align="center" | 4.0.3
| align="center" | 4.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview URL: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [http://www-users.cs.umn.edu/~moulitsa/software.html parmgridgen]
| align="center" | [http://www-users.cs.umn.edu/~moulitsa/software.html parmgridgen]
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| align="center" | bio
| align="center" | bio
| align="center" | 1.0.7, 1.7.0, 20170508
| align="center" | 1.0.7, 1.7.0, 20170508
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The pbbam software package provides components to create, query, and edit PacBio BAM files and associated indices. Homepage: http://pbbam.readthedocs.io/ URL: http://pbbam.readthedocs.io/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The pbbam software package provides components to create, query, and edit PacBio BAM files and associated indices. Homepage: http://pbbam.readthedocs.io/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/PacificBiosciences/pbcopper pbcopper]
| align="center" | [https://github.com/PacificBiosciences/pbcopper pbcopper]
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| align="center" | [https://www.perl.org/ perl]
| align="center" | [https://www.perl.org/ perl]
| align="center" | tools
| align="center" | tools
| align="center" | 5.16.3, 5.22.2, 5.22.4, 5.30.2
| align="center" | 5.16.3, 5.22.2, 5.22.4, 5.30.2, 5.36.1
| Documentation: [[Perl]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Algorithm::Dependency-1.111, Algorithm::Diff-1.1903, aliased-0.34, AnyEvent-7.17, App::Cmd-0.331, App::cpanminus-1.7044, AppConfig-1.71, Archive::Extract-0.86, Array::Utils-0.5, Authen::SASL-2.16, AutoLoader-5.74, B::Hooks::EndOfScope-0.24, B::Lint-1.20, boolean-0.46, Canary::Stability-2013, Capture::Tiny-0.48, Carp-1.50, Carp::Clan-6.08, Carp::Heavy-1.50, Class::Accessor-0.51, Class::Data::Inheritable-0.08, Class::DBI-v3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.36, Class::ISA-0.36, Class::Load-0.25, Class::Load::XS-0.10, Class::Singleton-1.5, Class::Trigger-0.14, Clone-0.43, Clone::Choose-0.010, Config::General-2.63, Config::INI-0.025, Config::MVP-2.200011, Config::Tiny-2.24, constant-1.33, CPANPLUS-0.9906, Crypt::DES-2.07, Crypt::Rijndael-1.14, Cwd-3.75, Cwd::Guard-0.05, Data::Dump-1.23, Data::Dumper-2.173, Data::Dumper::Concise-2.023, Data::Grove-0.08, Data::OptList-0.110, Data::Section-0.200007, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.17, Data::UUID-1.224, Date::Handler-1.2, Date::Language-2.32, DateTime-1.52, DateTime::Locale-1.25, DateTime::TimeZone-2.38, DateTime::Tiny-1.07, DBD::SQLite-1.64, DBI-1.643, DBIx::Admin::TableInfo-3.03, DBIx::ContextualFetch-1.03, DBIx::Simple-1.37, Devel::CheckCompiler-0.07, Devel::CheckLib-1.14, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.005, Devel::StackTrace-2.04, Digest::HMAC-1.03, Digest::MD5::File-0.08, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Dist::Zilla-6.014, Email::Date::Format-1.005, Encode-3.04, Encode::Locale-1.05, Error-0.17029, Eval::Closure-0.14, Exception::Class-1.44, Expect-1.35, Exporter-5.74, Exporter::Declare-0.114, Exporter::Tiny-1.002001, ExtUtils::CBuilder-0.280234, ExtUtils::Config-0.008, ExtUtils::Constant-0.25, ExtUtils::CppGuess-0.21, ExtUtils::Helpers-0.026, ExtUtils::InstallPaths-0.012, ExtUtils::MakeMaker-7.44, ExtUtils::ParseXS-3.35, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.45, File::Copy::Recursive::Reduced-0.006, File::Find::Rule-0.34, File::Find::Rule::Perl-1.15, File::Grep-0.02, File::HomeDir-1.004, File::Listing-6.04, File::Next-1.18, File::Path-2.16, File::pushd-1.016, File::Remove-1.58, File::ShareDir-1.116, File::ShareDir::Install-0.13, File::Slurp-9999.30, File::Slurp::Tiny-0.004, File::Slurper-0.012, File::Spec-3.75, File::Temp-0.2309, File::Which-1.23, Font::TTF-1.06, Getopt::Long-2.51, Getopt::Long::Descriptive-0.105, Git-0.42, GO-0.04, GO::Utils-0.15, Graph-0.9704, Graph::ReadWrite-2.09, Hash::Merge-0.300, HTML::Entities::Interpolate-1.10, HTML::Form-6.07, HTML::Parser-3.72, HTML::Tagset-3.20, HTML::Tree-5.07, HTTP::Cookies-6.08, HTTP::Daemon-6.06, HTTP::Date-6.05, HTTP::Negotiate-6.01, HTTP::Request-6.22, HTTP::Tiny-0.076, if-0.0608, Ima::DBI-0.35, Import::Into-1.002005, IO::File-1.42, IO::Handle-1.42, IO::HTML-1.001, IO::Seekable-1.42, IO::Select-1.42, IO::Socket-1.42, IO::Socket::SSL-2.067, IO::String-1.08, IO::Stringy-2.113, IO::Tty-1.14, IPC::Cmd-1.04, IPC::Run-20180523.0, IPC::Run3-0.048, JSON-4.02, Lingua::EN::PluralToSingular-0.21, List::AllUtils-0.16, List::MoreUtils-0.428, List::SomeUtils-0.58, List::Util-1.54, List::UtilsBy-0.11, Locale::Maketext::Simple-0.21, Log::Dispatch-2.69, Log::Dispatchouli-2.019, Log::Handler-0.88, Log::Log4perl-1.49, Log::Message-0.08, Log::Message::Simple-0.10, Logger::Simple-2.0, LWP::MediaTypes-6.04, LWP::Protocol::https-6.07, LWP::Simple-6.43, Mail::Util-2.21, Math::Bezier-0.01, Math::CDF-0.1, Math::Round-0.07, Math::VecStat-0.08, MCE::Mutex-1.866, Meta::Builder-0.004, MIME::Base64-3.15, MIME::Lite-3.031, MIME::Types-2.17, Mixin::Linewise::Readers-0.108, Mock::Quick-1.111, Module::Build-0.4231, Module::Build::Tiny-0.039, Module::Build::XSUtil-0.19, Module::CoreList-5.20200314, Module::Implementation-0.09, Module::Install-1.19, Module::Load-0.34, Module::Load::Conditional-0.70, Module::Metadata-1.000037, Module::Pluggable-5.2, Module::Runtime-0.016, Moo-2.003006, Moose-2.2012, MooseX::LazyRequire-0.11, MooseX::OneArgNew-0.005, MooseX::Role::Parameterized-1.11, MooseX::SetOnce-0.200002, MooseX::Types-0.50, MooseX::Types::Perl-0.101343, Mouse-v2.5.9, Mozilla::CA-20180117, MRO::Compat-0.13, namespace::autoclean-0.29, namespace::clean-0.27, Net::Domain-3.11, Net::HTTP-6.19, Net::SMTP::SSL-1.04, Net::SNMP-v6.0.1, Net::SSLeay-1.88, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Object::InsideOut-4.05, Package::Constants-0.06, Package::DeprecationManager-0.17, Package::Stash-0.38, Package::Stash::XS-0.29, Parallel::ForkManager-2.02, Params::Check-0.38, Params::Util-1.07, Params::Validate-1.29, Params::ValidationCompiler-0.30, parent-0.238, Parse::RecDescent-1.967015, Path::Tiny-0.112, PDF::API2-2.037, Perl::OSType-1.010, PerlIO::utf8_strict-0.007, Pod::Elemental-0.103005, Pod::Escapes-1.07, Pod::Eventual-0.094001, Pod::LaTeX-0.61, Pod::Man-4.14, Pod::Plainer-1.04, Pod::POM-2.01, Pod::Simple-3.40, Pod::Weaver-4.015, Readonly-2.05, Regexp::Common-2017060201, Role::HasMessage-0.006, Role::Identifiable::HasIdent-0.007, Role::Tiny-2.001004, Scalar::List::Utils-1.54, Scalar::Util-1.54, Scalar::Util::Numeric-0.40, Set::Array-0.30, Set::IntervalTree-0.12, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Scalar-1.29, Shell-0.73, Socket-2.029, Software::License-0.103014, Specio-0.46, SQL::Abstract-1.86, SQL::Statement-1.412, Statistics::Basic-1.6611, Statistics::Descriptive-3.0702, Storable-3.15, strictures-2.000006, String::Flogger-1.101245, String::RewritePrefix-0.008, String::Truncate-1.100602, Sub::Exporter-0.987, Sub::Exporter::ForMethods-0.100052, Sub::Exporter::Progressive-0.001013, Sub::Identify-0.14, Sub::Install-0.928, Sub::Name-0.26, Sub::Quote-2.006006, Sub::Uplevel-0.2800, Sub::Uplevel-0.2800, SVG-2.84, Switch-2.17, Template-3.007, Template::Plugin::Number::Format-1.06, Term::Encoding-0.03, Term::ReadKey-2.38, Term::ReadLine::Gnu-1.36, Term::UI-0.46, Test-1.26, Test::ClassAPI-1.07, Test::Deep-1.130, Test::Differences-0.67, Test::Exception-0.43, Test::Fatal-0.014, Test::Harness-3.42, Test::LeakTrace-0.16, Test::More-1.302172, Test::Most-0.35, Test::NoWarnings-1.04, Test::Output-1.031, Test::Pod-1.52, Test::Requires-0.10, Test::RequiresInternet-0.05, Test::Simple-1.302172, Test::Version-2.09, Test::Warn-0.36, Test::Warnings-0.029, Text::Aligner-0.13, Text::Balanced-2.03, Text::CSV-2.00, Text::Diff-1.45, Text::Format-0.61, Text::Glob-0.11, Text::Iconv-1.7, Text::ParseWords-3.30, Text::Soundex-3.05, Text::Table-1.133, Text::Template-1.58, Thread::Queue-3.13, Throwable-0.200013, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9760, Time::Local-1.30, Time::Piece-1.34, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.31, Try::Tiny-0.30, UNIVERSAL::moniker-0.08, URI-1.76, URI::Escape-3.31, version-0.9924, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::Filter::BufferText-1.01, XML::NamespaceSupport-1.12, XML::Parser-2.46, XML::RegExp-0.04, XML::SAX-1.02, XML::SAX::Base-1.09, XML::SAX::Writer-0.57, XML::Simple-2.25, XML::Tiny-2.07, XML::Twig-3.52, XML::XPath-1.44, XSLoader-0.24, YAML-1.30, YAML::Tiny-1.73 Keyword:tools<br /><br /><br /></div>
| Documentation: [[Perl]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Algorithm::Dependency-1.112, Algorithm::Diff-1.201, aliased-0.34, AnyEvent-7.17, App::Cmd-0.335, App::cpanminus-1.7046, AppConfig-1.71, Archive::Extract-0.88, Array::Transpose-0.06, Array::Utils-0.5, Authen::NTLM-1.09, Authen::SASL-2.16, AutoLoader-5.74, B::COW-0.007, B::Hooks::EndOfScope-0.26, B::Lint-1.20, boolean-0.46, Business::ISBN-3.008, Business::ISBN::Data-20230516.001, Canary::Stability-2013, Capture::Tiny-0.48, Carp-1.50, Carp::Clan-6.08, Carp::Heavy-1.50, CGI-4.57, Class::Accessor-0.51, Class::Data::Inheritable-0.09, Class::DBI-v3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.36, Class::ISA-0.36, Class::Load-0.25, Class::Load::XS-0.10, Class::Method::Modifiers-2.15, Class::Singleton-1.6, Class::Tiny-1.008, Class::Trigger-0.15, Class::XSAccessor-1.19, Clone-0.46, Clone::Choose-0.010, common::sense-3.75, Compress::Raw::Zlib-2.204, Config::General-2.65, Config::INI-0.029, Config::MVP-2.200013, Config::MVP::Reader::INI-2.101465, Config::Simple-4.58, Config::Tiny-2.29, Const::Exporter-1.2.2, Const::Fast-0.014, constant-1.33, CPAN::Meta::Check-0.017, CPAN::Uploader-0.103018, CPANPLUS-0.9914, Crypt::DES-2.07, Crypt::Rijndael-1.16, Cwd-3.75, Cwd::Guard-0.05, Data::Dump-1.25, Data::Dumper-2.183, Data::Dumper::Concise-2.023, Data::Grove-0.08, Data::OptList-0.114, Data::Section-0.200008, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.17, Data::UUID-1.226, Date::Handler-1.2, Date::Language-2.33, DateTime-1.59, DateTime::Locale-1.38, DateTime::TimeZone-2.60, DateTime::Tiny-1.07, DBD::CSV-0.60, DBD::SQLite-1.72, DBI-1.643, DBIx::Admin::CreateTable-2.11, DBIx::Admin::DSNManager-2.02, DBIx::Admin::TableInfo-3.04, DBIx::ContextualFetch-1.03, DBIx::Simple-1.37, Devel::CheckCompiler-0.07, Devel::CheckLib-1.16, Devel::Cycle-1.12, Devel::FindPerl-0.016, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.007, Devel::Size-0.83, Devel::StackTrace-2.04, Digest::HMAC-1.04, Digest::MD5::File-0.08, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Dist::Zilla-6.030, Email::Date::Format-1.008, Encode-3.19, Encode::Locale-1.05, Error-0.17029, Eval::Closure-0.14, Exception::Class-1.45, Expect-1.35, Exporter-5.77, Exporter::Declare-0.114, Exporter::Tiny-1.006002, ExtUtils::CBuilder-0.280236, ExtUtils::Config-0.008, ExtUtils::Constant-0.25, ExtUtils::CppGuess-0.26, ExtUtils::Helpers-0.026, ExtUtils::InstallPaths-0.012, ExtUtils::MakeMaker-7.70, ExtUtils::ParseXS-3.44, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.45, File::Copy::Recursive::Reduced-0.006, File::Find::Rule-0.34, File::Find::Rule::Perl-1.16, File::Grep-0.02, File::HomeDir-1.006, File::Listing-6.15, File::Next-1.18, File::Path-2.18, File::pushd-1.016, File::Remove-1.61, File::ShareDir-1.118, File::ShareDir::Install-0.14, File::Slurp-9999.32, File::Slurp::Tiny-0.004, File::Slurper-0.014, File::Spec-3.75, File::Temp-0.2311, File::Which-1.27, Font::TTF-1.06, Getopt::Long-2.54, Getopt::Long::Descriptive-0.111, Git-0.42, GO-0.04, GO::Utils-0.15, Graph-0.9726, Graph::ReadWrite-2.10, Hash::Merge-0.302, Hash::Objectify-0.008, Heap-0.80, Hook::LexWrap-0.26, HTML::Entities::Interpolate-1.10, HTML::Form-6.11, HTML::Parser-3.81, HTML::Tagset-3.20, HTML::Template-2.97, HTML::Tree-5.07, HTTP::CookieJar-0.014, HTTP::Cookies-6.10, HTTP::Daemon-6.16, HTTP::Date-6.05, HTTP::Message-6.44, HTTP::Negotiate-6.01, HTTP::Tiny-0.082, if-0.0608, Ima::DBI-0.35, Import::Into-1.002005, Importer-0.026, Inline-0.86, IO::Compress::Zip-2.204, IO::File-1.51, IO::HTML-1.004, IO::Socket::SSL-2.083, IO::String-1.08, IO::Stringy-2.113, IO::TieCombine-1.005, IO::Tty-1.17, IO::Tty-1.17, IPC::Cmd-1.04, IPC::Run-20220807.0, IPC::Run3-0.048, IPC::System::Simple-1.30, JSON-4.10, JSON::MaybeXS-1.004005, JSON::XS-4.03, Lingua::EN::PluralToSingular-0.21, List::AllUtils-0.19, List::MoreUtils-0.430, List::MoreUtils::XS-0.430, List::SomeUtils-0.59, List::UtilsBy-0.12, local::lib-2.000029, Locale::Maketext::Simple-0.21, Log::Dispatch-2.71, Log::Dispatch::Array-1.005, Log::Dispatchouli-3.002, Log::Handler-0.90, Log::Log4perl-1.57, Log::Message-0.08, Log::Message::Simple-0.10, Log::Report-1.34, Log::Report::Optional-1.07, Logger::Simple-2.0, LWP::MediaTypes-6.04, LWP::Protocol::https-6.10, LWP::Simple-6.70, Mail::Util-2.21, Math::Bezier-0.01, Math::CDF-0.1, Math::Round-0.07, Math::Utils-1.14, Math::VecStat-0.08, MCE::Mutex-1.884, Meta::Builder-0.004, MIME::Base64-3.16, MIME::Charset-v1.013.1, MIME::Lite-3.033, MIME::Types-2.24, Mixin::Linewise::Readers-0.111, Mock::Quick-1.111, Module::Build-0.4234, Module::Build::Tiny-0.045, Module::Build::XSUtil-0.19, Module::CoreList-5.20230423, Module::Implementation-0.09, Module::Install-1.21, Module::Load-0.36, Module::Load::Conditional-0.74, Module::Metadata-1.000038, Module::Path-0.19, Module::Path-0.19, Module::Pluggable-5.2, Module::Runtime-0.016, Module::Runtime::Conflicts-0.003, Moo-2.005005, Moose-2.2203, MooseX::LazyRequire-0.11, MooseX::OneArgNew-0.007, MooseX::Role::Parameterized-1.11, MooseX::SetOnce-0.203, MooseX::Types-0.50, MooseX::Types::Perl-0.101344, Mouse-v2.5.10, Mozilla::CA-20221114, MRO::Compat-0.15, namespace::autoclean-0.29, namespace::clean-0.27, Net::Domain-3.15, Net::HTTP-6.22, Net::SMTP::SSL-1.04, Net::SNMP-v6.0.1, Net::SSLeay-1.92, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Object::InsideOut-4.05, Object::InsideOut-4.05, Package::Constants-0.06, Package::DeprecationManager-0.18, Package::Stash-0.40, Package::Stash::XS-0.30, PadWalker-2.5, Parallel::ForkManager-2.02, Params::Check-0.38, Params::Util-1.102, Params::Validate-1.31, Params::ValidationCompiler-0.31, parent-0.241, Parse::RecDescent-1.967015, Parse::Yapp-1.21, Path::Tiny-0.144, PDF::API2-2.044, Perl::OSType-1.010, Perl::PrereqScanner-1.100, PerlIO::utf8_strict-0.010, Pod::Elemental-0.103006, Pod::Escapes-1.07, Pod::Eventual-0.094003, Pod::LaTeX-0.61, Pod::Man-5.01, Pod::Parser-1.66, Pod::Plainer-1.04, Pod::POM-2.01, Pod::Simple-3.45, Pod::Weaver-4.019, PPI-1.276, Readonly-2.05, Ref::Util-0.204, Regexp::Common-2017060201, Role::HasMessage-0.007, Role::Identifiable::HasIdent-0.009, Role::Tiny-2.002004, Scalar::Util-1.63, Scalar::Util::Numeric-0.40, Scope::Guard-0.21, Set::Array-0.30, Set::IntervalTree-0.12, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Object-1.42, Set::Scalar-1.29, Shell-0.73, Socket-2.036, Software::License-0.104003, Specio-0.48, Spiffy-0.46, SQL::Abstract-2.000001, SQL::Statement-1.414, Statistics::Basic-1.6611, Statistics::Descriptive-3.0800, Storable-3.25, strictures-2.000006, String::Errf-0.009, String::Flogger-1.101246, String::Formatter-1.235, String::Print-0.94, String::RewritePrefix-0.009, String::Truncate-1.100603, String::TtyLength-0.03, Sub::Exporter-0.989, Sub::Exporter::ForMethods-0.100055, Sub::Exporter::GlobExporter-0.006, Sub::Exporter::Progressive-0.001013, Sub::Identify-0.14, Sub::Info-0.002, Sub::Install-0.929, Sub::Name-0.27, Sub::Quote-2.006008, Sub::Uplevel-0.2800, SVG-2.87, Switch-2.17, Sys::Info-0.7811, Sys::Info::Base-0.7807, Sys::Info::Driver::Linux-0.7905, Sys::Info::Driver::Linux::Device::CPU-0.7905, Sys::Info::Driver::Unknown-0.79, Sys::Info::Driver::Unknown::Device::CPU-0.79, Template-3.101, Template::Plugin::Number::Format-1.06, Term::Encoding-0.03, Term::ReadKey-2.38, Term::ReadLine::Gnu-1.45, Term::Table-0.016, Term::UI-0.50, Test-1.26, Test2::Plugin::NoWarnings-0.09, Test2::Require::Module-0.000155, Test::Base-0.89, Test::CheckDeps-0.010, Test::ClassAPI-1.07, Test::CleanNamespaces-0.24, Test::Deep-1.204, Test::Differences-0.69, Test::Exception-0.43, Test::FailWarnings-0.008, Test::Fatal-0.017, Test::File-1.993, Test::File::ShareDir::Dist-1.001002, Test::Harness-3.44, Test::LeakTrace-0.17, Test::Memory::Cycle-1.06, Test::More::UTF8-0.05, Test::Most-0.38, Test::Needs-0.002010, Test::NoWarnings-1.06, Test::Object-0.08, Test::Output-1.033, Test::Pod-1.52, Test::Requires-0.11, Test::RequiresInternet-0.05, Test::Simple-1.302195, Test::SubCalls-1.10, Test::Sys::Info-0.23, Test::Version-2.09, Test::Warn-0.37, Test::Warnings-0.031, Test::Without::Module-0.21, Test::YAML-1.07, Text::Aligner-0.16, Text::Balanced-2.06, Text::CSV-2.02, Text::CSV_XS-1.50, Text::Diff-1.45, Text::Format-0.62, Text::Glob-0.11, Text::Iconv-1.7, Text::ParseWords-3.31, Text::Soundex-3.05, Text::Table-1.135, Text::Table::Manifold-1.03, Text::Template-1.61, Thread::Queue-3.13, threads-2.21, Throwable-1.001, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9764, Time::Local-1.35, Time::Piece-1.3401, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.32, Try::Tiny-0.31, Type::Tiny-2.004000, Types::Serialiser-1.01, Types::Serialiser-1.01, Unicode::EastAsianWidth-12.0, Unicode::LineBreak-2019.001, UNIVERSAL::moniker-0.08, Unix::Processors-2.046, Unix::Processors-2.046, URI-5.19, Variable::Magic-0.63, version-0.9929, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::Filter::BufferText-1.01, XML::NamespaceSupport-1.12, XML::Parser-2.46, XML::RegExp-0.04, XML::SAX-1.02, XML::SAX::Base-1.09, XML::SAX::Expat-0.51, XML::SAX::Writer-0.57, XML::Simple-2.25, XML::Tiny-2.07, XML::Twig-3.52, XML::Writer-0.900, XML::XPath-1.48, XSLoader-0.24, YAML-1.30, YAML::Tiny-1.74 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://metacpan.org/pod/Perl4::CoreLibs perl4-corelibs]
| align="center" | [https://metacpan.org/pod/Perl4::CoreLibs perl4-corelibs]
Line 3,817: Line 3,902:
| align="center" | [http://www.mcs.anl.gov/petsc petsc]
| align="center" | [http://www.mcs.anl.gov/petsc petsc]
| align="center" | tools
| align="center" | tools
| align="center" | 3.7.5, 3.10.2, 3.10.5, 3.11.3, 3.12.0, 3.12.4, 3.13.3, 3.13.6, 3.14.1, 3.15.0, 3.17.1, 3.19.2
| align="center" | 3.7.5, 3.10.2, 3.10.5, 3.11.3, 3.12.0, 3.12.4, 3.13.3, 3.13.6, 3.14.1, 3.15.0, 3.17.1, 3.19.2, 3.20.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: petsc4py-3.19.2 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.10, python/3.11 Extensions: petsc4py-3.20.0 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc-64bits]
| align="center" | [http://www.mcs.anl.gov/petsc petsc-64bits]
Line 3,827: Line 3,912:
| align="center" | [http://www.mcs.anl.gov/petsc petsc-complex]
| align="center" | [http://www.mcs.anl.gov/petsc petsc-complex]
| align="center" | tools
| align="center" | tools
| align="center" | 3.10.2, 3.11.3
| align="center" | 3.10.2, 3.11.3, 3.20.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Homepage: http://www.mcs.anl.gov/petsc URL: http://www.mcs.anl.gov/petsc Compatible modules: python/3.10, python/3.11 Extensions: petsc4py-3.20.0 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc-pardiso]
| align="center" | [http://www.mcs.anl.gov/petsc petsc-pardiso]
Line 3,852: Line 3,937:
| align="center" | [https://www.pflotran.org/ pflotran]
| align="center" | [https://www.pflotran.org/ pflotran]
| align="center" | -
| align="center" | -
| align="center" | 4.0
| align="center" | 4.0, 5.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PFLOTRAN is an open source, state-of-the-art massively parallel subsurface flow and reactive transport code. PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops. Homepage: https://www.pflotran.org/ URL: https://www.pflotran.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PFLOTRAN is an open source, state-of-the-art massively parallel subsurface flow and reactive transport code. PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops. Homepage: https://www.pflotran.org/ URL: https://www.pflotran.org/<br /><br /><br /></div>
|-
|-
Line 3,879: Line 3,964:
| align="center" | 1.48
| align="center" | 1.48
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The program PHON calculates force constant matrices and phonon frequencies in crystals. From the frequencies it also calculates various thermodynamic quantities, like the Helmholtz free energy, the entropy, the specific heat and the internal energy of the harmonic crystal. The procedure is based on the small displacement method, and can be used in combination with any program capable to calculate forces on the atoms of the crystal. Homepage: http://www.homepages.ucl.ac.uk/~ucfbdxa/phon/ URL: http://www.homepages.ucl.ac.uk/~ucfbdxa/phon/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The program PHON calculates force constant matrices and phonon frequencies in crystals. From the frequencies it also calculates various thermodynamic quantities, like the Helmholtz free energy, the entropy, the specific heat and the internal energy of the harmonic crystal. The procedure is based on the small displacement method, and can be used in combination with any program capable to calculate forces on the atoms of the crystal. Homepage: http://www.homepages.ucl.ac.uk/~ucfbdxa/phon/ URL: http://www.homepages.ucl.ac.uk/~ucfbdxa/phon/<br /><br /><br /></div>
|-
| align="center" | [https://github.com/icecube/photospline photospline]
| align="center" | -
| align="center" | 2.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Detector response to a high-energy physics process is often estimated by Monte Carlo simulation. For purposes of data analysis, the results of this simulation are typically stored in large multi-dimensional histograms, which can quickly become unwieldy in terms of size or numerically problematic due to unfilled bins or interpolation artifacts. Photospline is a library that uses the penalized spline technique to efficiently compute, store, and evaluate B-spline representations of such tables. Homepage: https://github.com/icecube/photospline URL: https://github.com/icecube/photospline<br /><br /><br /></div>
|-
|-
| align="center" | [http://evolution.genetics.washington.edu/phylip phylip]
| align="center" | [http://evolution.genetics.washington.edu/phylip phylip]
Line 3,910: Line 4,000:
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: phyx performs phylogenetics analyses on trees and sequences. Homepage: https://github.com/FePhyFoFum/phyx URL: https://github.com/FePhyFoFum/phyx Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: phyx performs phylogenetics analyses on trees and sequences. Homepage: https://github.com/FePhyFoFum/phyx URL: https://github.com/FePhyFoFum/phyx Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://samtools.github.io/hts-specs) picard]
| align="center" | [https://broadinstitute.github.io/picard/ picard]
| align="center" | bio
| align="center" | bio
| align="center" | 2.1.1, 2.10.7, 2.17.3, 2.18.9, 2.20.6, 2.23.2, 2.23.3, 2.26.3
| align="center" | 2.1.1, 2.10.7, 2.17.3, 2.18.9, 2.20.6, 2.23.2, 2.23.3, 2.26.3, 3.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ URL: http://broadinstitute.github.io/picard/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A set of tools (in Java) for working with next generation sequencing data in the BAM format. Homepage: https://broadinstitute.github.io/picard/ URL: https://broadinstitute.github.io/picard/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.drive5.com/pilercr/ pilercr]
| align="center" | [https://www.drive5.com/pilercr/ pilercr]
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| align="center" | bio
| align="center" | bio
| align="center" | 1.22, 1.23, 1.24
| align="center" | 1.22, 1.23, 1.24
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pilon is an automated genome assembly improvement and variant detection tool To run pilon, please use: java -jar $EBROOTPILON/pilon-1.23.jar ... Use -Xmx Java option to adjust memory as in: java -Xmx8G -jar $EBROOTPILON/pilon-1.23.jar ... Homepage: https://github.com/broadinstitute/pilon Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pilon is an automated genome assembly improvement and variant detection tool Homepage: https://github.com/broadinstitute/pilon URL: https://github.com/broadinstitute/pilon Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://gmt.genome.wustl.edu/packages/pindel/ pindel]
| align="center" | [http://gmt.genome.wustl.edu/packages/pindel/ pindel]
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| align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink]
| align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink]
| align="center" | bio
| align="center" | bio
| align="center" | 1.9b_4.1-x86_64, 1.9b_5.2-x86_64, 1.9b_6.21-x86_64, 2.00a2.3_x86_64, 2.00a3.6, 2.00-10252019-avx2, 1.07
| align="center" | 1.9b_4.1-x86_64, 1.9b_5.2-x86_64, 1.9b_6.21-x86_64, 2.00a2.3_x86_64, 2.00a3.6, 2.00a5.8, 2.00-10252019-avx2, 2.00-20231024-avx2, 1.07
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Keyword:bio<br /><br /><br /></div>
|-
|-
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer. Homepage: http://plplot.sourceforge.net URL: http://plplot.sourceforge.net Compatible modules: python/3.6, python/3.7<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer. Homepage: http://plplot.sourceforge.net URL: http://plplot.sourceforge.net Compatible modules: python/3.6, python/3.7<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.plumed-code.org plumed]
| align="center" | [https://www.plumed.org plumed]
| align="center" | chem
| align="center" | chem
| align="center" | 2.3.7, 2.4.2, 2.4.3, 2.5.2, 2.5.3, 2.5.4, 2.6.1, 2.6.2, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.7.6, 2.8.1, 2.8.3
| align="center" | 2.3.7, 2.4.2, 2.4.3, 2.5.2, 2.5.3, 2.5.4, 2.6.1, 2.6.2, 2.7.0, 2.7.1, 2.7.2, 2.7.3, 2.7.4, 2.7.6, 2.8.1, 2.8.3, 2.9.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. This module has been compiled with additional modules, and support for XDR-files (GROMACS XTC/TRR), Python, GSL, Boost-serialization, Boost-Graph and other optional features. To find out more, run 'plumed config show' after loading this module. Homepage: http://www.plumed-code.org URL: http://www.plumed-code.org Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. Homepage: https://www.plumed.org URL: https://www.plumed.org Compatible modules: python/3.10, python/3.11 Extensions: plumed-2.9.0 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://plutojl.org/ pluto]
| align="center" | [https://plutojl.org/ pluto]
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| align="center" | [https://pmix.org/ pmix]
| align="center" | [https://pmix.org/ pmix]
| align="center" | -
| align="center" | -
| align="center" | 1.2.5, 3.1.5, 3.2.3, 4.1.2
| align="center" | 1.2.5, 3.1.5, 3.2.3, 4.1.2, 4.2.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to resolve these questions by providing an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. Homepage: https://pmix.org/ URL: https://pmix.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. Homepage: https://pmix.org/ URL: https://pmix.org/<br /><br /><br /></div>
|-
|-
| align="center" | [https://trac.mcs.anl.gov/projects/parallel-netcdf pnetcdf]
| align="center" | [https://trac.mcs.anl.gov/projects/parallel-netcdf pnetcdf]
| align="center" | io
| align="center" | io
| align="center" | 1.9.0, 1.10.0, 1.12.2
| align="center" | 1.9.0, 1.10.0, 1.12.2, 1.12.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (&gt; 2B array elements). Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf URL: https://trac.mcs.anl.gov/projects/parallel-netcdf Keyword:io<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PnetCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidata's NetCDF, specifically the formats of CDF-1, 2, and 5. The CDF-5 file format, an extension of CDF-2, supports unsigned data types and uses 64-bit integers to allow users to define large dimensions, attributes, and variables (&gt; 2B array elements). Homepage: https://trac.mcs.anl.gov/projects/parallel-netcdf URL: https://trac.mcs.anl.gov/projects/parallel-netcdf Keyword:io<br /><br /><br /></div>
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| align="center" | [https://www.postgresql.org/ postgresql]
| align="center" | [https://www.postgresql.org/ postgresql]
| align="center" | tools
| align="center" | tools
| align="center" | 9.6.6, 10.2, 10.3, 11.6, 12.1, 12.4, 13.2, 14.2
| align="center" | 9.6.6, 10.2, 10.3, 11.6, 12.1, 12.4, 13.2, 14.2, 16.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Homepage: https://www.postgresql.org/ URL: https://www.postgresql.org/ Compatible modules: python/3.8, python/3.7, python/3.6, python/2.7 Extensions: psycopg2-2.8.6 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Homepage: https://www.postgresql.org/ URL: https://www.postgresql.org/ Compatible modules: python/3.10, python/3.11 Extensions: psycopg2-2.9.9 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.povray.org/ pov-ray]
| align="center" | [https://www.povray.org/ pov-ray]
| align="center" | -
| align="center" | -
| align="center" | 3.8.0-x.10064738, 3.7.0.7
| align="center" | 3.8.0-x.10064738, 3.7.0.7, 3.7.0.10
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. Homepage: http://www.povray.org/ URL: http://www.povray.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. Homepage: https://www.povray.org/ URL: https://www.povray.org/<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.povray.org/ povray]
| align="center" | [http://www.povray.org/ povray]
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| align="center" | [https://proj.org proj]
| align="center" | [https://proj.org proj]
| align="center" | geo
| align="center" | geo
| align="center" | 4.9.3, 5.1.0, 5.2.0, 6.0.0, 6.3.0, 6.3.2, 7.0.0, 7.0.1, 7.2.1, 8.0.0, 9.0.0, 9.0.1
| align="center" | 4.9.3, 5.1.0, 5.2.0, 6.0.0, 6.3.0, 6.3.2, 7.0.0, 7.0.1, 7.2.1, 8.0.0, 9.0.0, 9.0.1, 9.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: https://proj.org URL: https://proj.org Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: pyproj-3.3.0 Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: https://proj.org URL: https://proj.org Compatible modules: python/3.10, python/3.11 Extensions: pyproj-3.6.1 Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/mhagdorn/proj4-fortran proj4-fortran]
| align="center" | [https://github.com/mhagdorn/proj4-fortran proj4-fortran]
| align="center" | geo
| align="center" | geo
| align="center" | 1.0
| align="center" | 1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: proj4-fortran is a f77 and f90 wrappers for proj4, a cartograohic projections library. Homepage: https://github.com/mhagdorn/proj4-fortran URL: https://github.com/mhagdorn/proj4-fortran Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: proj4-fortran is a f77 and f90 wrappers for proj4, a cartograohic projections library. Homepage: https://github.com/mhagdorn/proj4-fortran Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.vicbioinformatics.com/software.prokka.shtml prokka]
| align="center" | [https://www.vicbioinformatics.com/software.prokka.shtml prokka]
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| align="center" | [https://github.com/google/protobuf/ protobuf]
| align="center" | [https://github.com/google/protobuf/ protobuf]
| align="center" | tools
| align="center" | tools
| align="center" | 3.3.0, 3.6.1, 3.7.1, 3.9.1, 3.11.1, 3.12.3, 3.19.4, 3.21.3
| align="center" | 3.3.0, 3.6.1, 3.7.1, 3.9.1, 3.11.1, 3.12.3, 3.19.4, 3.21.3, 24.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ URL: https://github.com/google/protobuf/ Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4, python/3.8.0 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/ URL: https://github.com/google/protobuf/ Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://psfex.readthedocs.io/en/latest/index.html psfex]
| align="center" | [https://psfex.readthedocs.io/en/latest/index.html psfex]
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| align="center" | [http://www.psicode.org/ psi4]
| align="center" | [http://www.psicode.org/ psi4]
| align="center" | chem
| align="center" | chem
| align="center" | 1.1, 1.3.2, 1.4, 1.5
| align="center" | 1.1, 1.3.2, 1.4, 1.5, 1.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. Homepage: http://www.psicode.org/ URL: http://www.psicode.org/ Compatible modules: python/3.7, python/3.8 Extensions: deepdiff-5.5.0, Pint-0.16.1, pydantic-1.7.3 Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. Homepage: http://www.psicode.org/ URL: http://www.psicode.org/ Compatible modules: python/3.10, python/3.11 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [http://bioinf.cs.ucl.ac.uk psipred]
| align="center" | [http://bioinf.cs.ucl.ac.uk psipred]
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| align="center" | bio
| align="center" | bio
| align="center" | 0.6.5
| align="center" | 0.6.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. Homepage: https://github.com/lh3/psmc URL: https://github.com/lh3/psmc Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. Homepage: https://github.com/lh3/psmc Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://ptex.us/ ptex]
| align="center" | [https://ptex.us/ ptex]
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| align="center" | -
| align="center" | -
| align="center" | 6.1.2, 6.2.5, 7.0.1, 7.4.0
| align="center" | 6.1.2, 6.2.5, 7.0.1, 7.4.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: pytest: simple powerful testing with Python Homepage: https://pytest.org URL: https://pytest.org Compatible modules: python/3.7, python/3.8, python/3.9, python/3.10 Extensions: attrs-21.2.0, execnet-1.9.0, iniconfig-1.1.1, packaging-21.0, pluggy-1.0.0, py-1.10.0, pyparsing-3.0.2, pytest-6.2.5, pytest-forked-1.3.0, pytest_mpi-0.5, pytest_xdist-2.4.0, toml-0.10.2<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: pytest: simple powerful testing with Python Homepage: https://pytest.org URL: https://pytest.org Compatible modules: python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Extensions: iniconfig-2.0.0, packaging-23.1, pluggy-1.2.0, py-1.11.0, pytest-7.4.0, tomli-2.0.1<br /><br /><br /></div>
|-
|-
| align="center" | [https://python.org/ python]
| align="center" | [https://python.org/ python]
| align="center" | tools
| align="center" | tools
| align="center" | 2.7.13, 2.7.14, 2.7.18, 3.5.2, 3.5.4, 3.6.3, 3.6.10, 3.7.0, 3.7.4, 3.7.7, 3.7.9, 3.8.0, 3.8.2, 3.8.10, 3.9.6, 3.10.2, 3.11.2, 3.11.5
| align="center" | 2.7.13, 2.7.14, 2.7.18, 3.5.2, 3.5.4, 3.6.3, 3.6.10, 3.7.0, 3.7.4, 3.7.7, 3.7.9, 3.8.0, 3.8.2, 3.8.10, 3.9.6, 3.10.2, 3.10.13, 3.11.2, 3.11.5
| Documentation: [[Python]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: https://python.org/ URL: https://python.org/ Extensions: distlib-0.3.7, editables-0.5, filelock-3.12.2, flit_core-3.9.0, hatch_vcs-0.3.0, hatchling-1.18.0, packaging-23.1, pathspec-0.11.2, pip-23.2.1, platformdirs-3.10.0, pluggy-1.3.0, pyparsing-3.1.1, setuptools-68.1.2, setuptools_scm-7.1.0, six-1.16.0, tomli-2.0.1, trove-classifiers-2023.8.7, typing_extensions-4.7.1, virtualenv-20.24.3, wheel-0.41.2 Keyword:tools<br /><br /><br /></div>
| Documentation: [[Python]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: https://python.org/ URL: https://python.org/ Extensions: distlib-0.3.7, editables-0.5, filelock-3.12.2, flit_core-3.9.0, hatch_vcs-0.3.0, hatchling-1.18.0, packaging-23.1, pathspec-0.11.2, pip-23.2.1, platformdirs-3.10.0, pluggy-1.3.0, pyparsing-3.1.1, setuptools-68.1.2, setuptools_scm-7.1.0, six-1.16.0, tomli-2.0.1, trove-classifiers-2023.8.7, typing_extensions-4.7.1, virtualenv-20.24.3, wheel-0.41.2 Keyword:tools<br /><br /><br /></div>
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| align="center" | -
| align="center" | -
| align="center" | 2022a, 2023a, 2023b
| align="center" | 2022a, 2023a, 2023b
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains Python packages useful for building Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.11, python/3.10, python/3.9, python/3.8 Extensions: archspec-0.2.1, cachecontrol-0.13.1, cachy-0.3.0, certifi-2023.7.22, cffi-1.15.1, charset-normalizer-3.2.0, cleo-2.0.1, clikit-0.6.2, crashtest-0.4.1, cryptography-41.0.3, distlib-0.3.7, distro-1.8.0, editables-0.5, exceptiongroup-1.1.3, filelock-3.12.2, flit-core-3.9.0, flit-scm-1.7.0, hatch_fancy_pypi_readme-23.1.0, hatch_vcs-0.3.0, hatchling-1.18.0, html5lib-1.1, idna-3.4, importlib_metadata-6.8.0, importlib_resources-6.0.1, jeepney-0.8.0, keyring-24.2.0, keyrings.alt-5.0.0, meson-1.2.1, meson_python-0.14.0, msgpack-1.0.5, ninja-1.11.1, packaging-23.1, pastel-0.2.1, pathspec-0.11.2, pbr-5.11.1, pexpect-4.8.0, pkginfo-1.9.6, platformdirs-3.10.0, poetry-1.6.1, poetry_core-1.7.0, ptyprocess-0.7.0, pybind11-2.11.1, pycparser-2.21, pylev-1.4.0, pyparsing-3.1.1, pyproject-metadata-0.7.1, pytoml-0.1.21, requests-2.31.0, requests-toolbelt-1.0.0, scikit_build-0.17.6, scikit_build_core-0.5.0, SecretStorage-3.3.3, semantic_version-2.10.0, setuptools-68.1.2, setuptools-rust-1.7.0, setuptools_scm-7.1.0, shellingham-1.5.3, toml-0.10.2, tomli-2.0.1, tomlkit-0.12.1, trove-classifiers-2023.8.7, typing_extensions-4.7.1, urllib3-2.0.4, virtualenv-20.24.3, webencodings-0.5.1, wheel-0.41.2, zipp-3.16.2<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains Python packages useful for building Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.11, python/3.10 Extensions: archspec-0.2.1, cachecontrol-0.13.1, cachy-0.3.0, certifi-2023.7.22, cffi-1.15.1, charset-normalizer-3.2.0, cleo-2.0.1, clikit-0.6.2, crashtest-0.4.1, cryptography-41.0.3, distlib-0.3.7, distro-1.8.0, editables-0.5, exceptiongroup-1.1.3, filelock-3.12.2, flit-core-3.9.0, flit-scm-1.7.0, hatch_fancy_pypi_readme-23.1.0, hatch_vcs-0.3.0, hatchling-1.18.0, html5lib-1.1, idna-3.4, importlib_metadata-6.8.0, importlib_resources-6.0.1, jeepney-0.8.0, keyring-24.2.0, keyrings.alt-5.0.0, meson-1.2.1, meson_python-0.14.0, msgpack-1.0.5, ninja-1.11.1, packaging-23.1, pastel-0.2.1, pathspec-0.11.2, pbr-5.11.1, pexpect-4.8.0, pkginfo-1.9.6, platformdirs-3.10.0, poetry-1.6.1, poetry_core-1.7.0, ptyprocess-0.7.0, pybind11-2.11.1, pycparser-2.21, pylev-1.4.0, pyparsing-3.1.1, pyproject-metadata-0.7.1, pytoml-0.1.21, requests-2.31.0, requests-toolbelt-1.0.0, scikit_build-0.17.6, scikit_build_core-0.5.0, SecretStorage-3.3.3, semantic_version-2.10.0, setuptools-68.1.2, setuptools-rust-1.7.0, setuptools_scm-7.1.0, shellingham-1.5.3, toml-0.10.2, tomli-2.0.1, tomlkit-0.12.1, trove-classifiers-2023.8.7, typing_extensions-4.7.1, urllib3-2.0.4, virtualenv-20.24.3, webencodings-0.5.1, wheel-0.41.2, zipp-3.16.2<br /><br /><br /></div>
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|-
| align="center" | [http://delta.affinix.com/qca/ qca]
| align="center" | [https://userbase.kde.org/QCA qca]
| align="center" | geo
| align="center" | geo
| align="center" | 2.1.3, 2.3.0, 2.3.5
| align="center" | 2.1.3, 2.3.0, 2.3.5, 2.3.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. Homepage: http://delta.affinix.com/qca/ URL: http://delta.affinix.com/qca/ Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. Homepage: https://userbase.kde.org/QCA URL: https://userbase.kde.org/QCA Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [http://wiki.sunqm.net/libcint qcint]
| align="center" | [http://wiki.sunqm.net/libcint qcint]
| align="center" | -
| align="center" | -
| align="center" | 4.4.6, 5.1.5, 5.1.7, 5.1.8
| align="center" | 4.4.6, 5.1.5, 5.1.7, 5.1.8, 6.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform. Homepage: http://wiki.sunqm.net/libcint URL: http://wiki.sunqm.net/libcint<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform. Homepage: http://wiki.sunqm.net/libcint URL: http://wiki.sunqm.net/libcint<br /><br /><br /></div>
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| align="center" | [http://www.qgis.org/ qgis]
| align="center" | [http://www.qgis.org/ qgis]
| align="center" | geo
| align="center" | geo
| align="center" | 2.18.24, 3.10.6, 3.22.14
| align="center" | 2.18.24, 3.10.6, 3.22.14, 3.28.12
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QGIS is a user friendly Open Source Geographic Information System (GIS) Homepage: http://www.qgis.org/ URL: http://www.qgis.org/ Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: OWSLib-0.20.0, psycopg2-2.8.5, pyproj-2.6.1.post1, PyYAML-5.3.1 Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QGIS is a user friendly Open Source Geographic Information System (GIS) Homepage: http://www.qgis.org/ URL: http://www.qgis.org/ Compatible modules: python/3.11, python/3.10 Extensions: OWSLib-0.29.3, psycopg2-2.9.9, PyYAML-6.0.1 Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.qhull.org qhull]
| align="center" | [http://www.qhull.org qhull]
| align="center" | math
| align="center" | math
| align="center" | 2015.2, 2019.1
| align="center" | 2015.2, 2019.1, 2020.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Homepage: http://www.qhull.org URL: http://www.qhull.org Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Homepage: http://www.qhull.org URL: http://www.qhull.org Keyword:math<br /><br /><br /></div>
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| align="center" | math
| align="center" | math
| align="center" | 1.1.2
| align="center" | 1.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. Homepage: https://sourceforge.net/projects/qrupdate/ URL: https://sourceforge.net/projects/qrupdate/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. Homepage: https://sourceforge.net/projects/qrupdate/ Keyword:math<br /><br /><br /></div>
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|-
| align="center" | [https://www.riverbankcomputing.com/software/qscintilla qscintilla]
| align="center" | [https://www.riverbankcomputing.com/software/qscintilla qscintilla]
| align="center" | tools
| align="center" | tools
| align="center" | 2.10.7, 2.11.2, 2.11.6
| align="center" | 2.10.7, 2.11.2, 2.11.6, 2.14.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control Homepage: https://www.riverbankcomputing.com/software/qscintilla URL: https://www.riverbankcomputing.com/software/qscintilla Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control Homepage: https://www.riverbankcomputing.com/software/qscintilla URL: https://www.riverbankcomputing.com/software/qscintilla Compatible modules: python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://qt.io/ qt]
| align="center" | [https://qt.io/ qt]
| align="center" | tools
| align="center" | tools
| align="center" | 3.3.8, 4.8.7, 5.6.1, 5.9.6, 5.10.1, 5.11.3, 5.12.3, 5.12.8, 5.13.1, 5.15.2, 5.15.8
| align="center" | 3.3.8, 4.8.7, 5.6.1, 5.9.6, 5.10.1, 5.11.3, 5.12.3, 5.12.8, 5.13.1, 5.15.2, 5.15.8, 5.15.11
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: https://qt.io/ URL: https://qt.io/ Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: packaging-21.3, PyQt-builder-1.11.0, PyQt5-5.15.5, PyQt5_sip-12.11.0, PyQtWebEngine-5.15.6, SIP-5.5.0, toml-0.10.2 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: https://qt.io/ URL: https://qt.io/ Compatible modules: python/3.10, python/3.11 Extensions: ply-3.11, PyQt-builder-1.15.3, PyQt5-5.15.10, PyQt5_sip-12.13.0, PyQtWebEngine-5.15.6, SIP-6.7.12, toml-0.10.2 Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://github.com/qt/qtwebkit qt5webkit]
| align="center" | [https://github.com/qt/qtwebkit qt5webkit]
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| align="center" | [https://github.com/frankosterfeld/qtkeychain qtkeychain]
| align="center" | [https://github.com/frankosterfeld/qtkeychain qtkeychain]
| align="center" | -
| align="center" | -
| align="center" | 0.9.1, 0.13.2
| align="center" | 0.9.1, 0.13.2, 0.14.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Platform-independent Qt API for storing passwords securely. Homepage: https://github.com/frankosterfeld/qtkeychain URL: https://github.com/frankosterfeld/qtkeychain<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Platform-independent Qt API for storing passwords securely. Homepage: https://github.com/frankosterfeld/qtkeychain URL: https://github.com/frankosterfeld/qtkeychain<br /><br /><br /></div>
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QuantumATK is a complete atomistic simulation toolkit. QuantumATK addresses key applications in the semiconductor industry and is a core component of the Synopsys Design-Technology Co-Optimization (DTCO) solution. Atomic-scale modeling tools in QuantumATK range from classical force fields for handling large and to some extent more realistic materials systems to ab initio tools that provide highly accurate results for smaller systems. Homepage: https://www.synopsys.com/silicon/quantumatk.html URL: https://www.synopsys.com/silicon/quantumatk.html<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QuantumATK is a complete atomistic simulation toolkit. QuantumATK addresses key applications in the semiconductor industry and is a core component of the Synopsys Design-Technology Co-Optimization (DTCO) solution. Atomic-scale modeling tools in QuantumATK range from classical force fields for handling large and to some extent more realistic materials systems to ab initio tools that provide highly accurate results for smaller systems. Homepage: https://www.synopsys.com/silicon/quantumatk.html URL: https://www.synopsys.com/silicon/quantumatk.html<br /><br /><br /></div>
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| align="center" | [http://www.pwscf.org/ quantumespresso]
| align="center" | [https://www.quantum-espresso.org quantumespresso]
| align="center" | chem
| align="center" | chem
| align="center" | 6.2.2, 6.3, 6.4.1, 6.5, 6.6, 6.7, 6.8, 7.0, 7.1, 7.2
| align="center" | 6.2.2, 6.3, 6.4.1, 6.5, 6.6, 6.7, 6.8, 7.0, 7.1, 7.2
| Documentation: [[Quantum ESPRESSO]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). This module includes thermo_pw add-on package. Homepage: http://www.pwscf.org/ URL: http://www.pwscf.org/ Keyword:chem<br /><br /><br /></div>
| Documentation: [[Quantum ESPRESSO]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Homepage: https://www.quantum-espresso.org URL: https://www.quantum-espresso.org Keyword:chem<br /><br /><br /></div>
|-
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| align="center" | [https://github.com/ablab/quast quast]
| align="center" | [https://github.com/ablab/quast quast]
| align="center" | -
| align="center" | -
| align="center" | 5.0.2, 5.2.0
| align="center" | 5.0.2, 5.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Homepage: https://github.com/ablab/quast URL: https://github.com/ablab/quast Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: joblib-0.17.0, QUAST-5.0.2, semantic-version-2.8.5, setuptools-rust-0.11.6, simplejson-3.17.0, toml-0.10.2<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Homepage: https://github.com/ablab/quast URL: https://github.com/ablab/quast Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: joblib-0.17.0, QUAST-5.2.0, semantic-version-2.8.5, simplejson-3.17.0, toml-0.10.2<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.genome.umd.edu/quorum.html quorum]
| align="center" | [http://www.genome.umd.edu/quorum.html quorum]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QuorUM is an error corrector for Illumina reads Homepage: http://www.genome.umd.edu/quorum.html Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QuorUM is an error corrector for Illumina reads Homepage: http://www.genome.umd.edu/quorum.html Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://qwt.sourceforge.net/ qwt]
| align="center" | [http://qwt.sourceforge.net/ qwt]
| align="center" | tools
| align="center" | tools
| align="center" | 6.1.3, 6.1.4, 6.2.0
| align="center" | 6.1.3, 6.1.4, 6.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: https://qwt.sourceforge.net/ URL: https://qwt.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: http://qwt.sourceforge.net/ URL: http://qwt.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://qwtpolar.sourceforge.net/ qwtpolar]
| align="center" | [http://qwtpolar.sourceforge.net/ qwtpolar]
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| align="center" | [https://bioconductor.org r-bundle-bioconductor]
| align="center" | [https://bioconductor.org r-bundle-bioconductor]
| align="center" | bio
| align="center" | bio
| align="center" | 3.8, 3.9, 3.12, 3.14, 3.16, 3.17
| align="center" | 3.8, 3.9, 3.12, 3.14, 3.16, 3.17, 3.18
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. Homepage: https://bioconductor.org URL: https://bioconductor.org Extensions: abind-1.4-5, ade4-1.7-22, admisc-0.33, affxparser-1.72.0, affy-1.78.2, affycoretools-1.72.0, affyio-1.70.0, AgiMicroRna-2.50.0, agricolae-1.3-6, ALDEx2-1.32.0, AlgDesign-1.2.1, ALL-1.42.0, annaffy-1.72.0, annotate-1.78.0, AnnotationDbi-1.62.2, AnnotationFilter-1.24.0, AnnotationForge-1.42.2, AnnotationHub-3.8.0, anytime-0.3.9, aod-1.3.2, ape-5.7-1, aroma.affymetrix-3.2.1, aroma.apd-0.7.0, aroma.core-3.3.0, aroma.light-3.30.0, ash-1.0-15, askpass-1.1, assertthat-0.2.1, ATACseqQC-1.24.0, aws-2.5-3, aws.s3-0.3.21, aws.signature-0.6.0, awsMethods-1.1-1, backports-1.4.1, ballgown-2.32.0, base64-2.0.1, base64enc-0.1-3, basilisk-1.12.1, basilisk.utils-1.12.1, batchelor-1.16.0, baySeq-2.34.0, BBmisc-1.13, beachmat-2.16.0, beanplot-1.3.1, beeswarm-0.4.0, BH-1.81.0-1, BiasedUrn-2.0.10, Biobase-2.60.0, BiocBaseUtils-1.2.0, BiocFileCache-2.8.0, BiocGenerics-0.46.0, BiocIO-1.10.0, BiocManager-1.30.22, BiocNeighbors-1.18.0, BiocParallel-1.34.2, BiocSingular-1.16.0, BiocStyle-2.28.0, BiocVersion-3.17.1, biomaRt-2.56.1, biomformat-1.28.0, Biostrings-2.68.1, biovizBase-1.48.0, bit-4.0.5, bit64-4.0.5, bitops-1.0-7, blme-1.0-5, blob-1.2.4, bluster-1.10.0, bookdown-0.35, boot-1.3-28.1, brio-1.1.3, broom-1.0.5, BSgenome-1.68.0, BSgenome.Cfamiliaris.UCSC.canFam3-1.4.0, BSgenome.Hsapiens.UCSC.hg19-1.4.3, BSgenome.Hsapiens.UCSC.hg38-1.4.5, BSgenome.Mmusculus.UCSC.mm10-1.4.3, bslib-0.5.1, bumphunter-1.42.0, ca-0.71.1, cachem-1.0.8, Cairo-1.6-0, calibrate-1.7.7, callr-3.7.3, CAMERA-1.56.0, car-3.1-2, carData-3.0-5, caret-6.0-94, Category-2.66.0, caTools-1.18.2, ccdata-1.26.0, ccmap-1.26.0, cellranger-1.1.0, CGHbase-1.60.0, checkmate-2.2.0, ChIPpeakAnno-3.34.1, circlize-0.4.15, class-7.3-22, classInt-0.4-9, cli-3.6.1, clipr-0.8.0, clock-0.7.0, clue-0.3-64, cluster-2.1.4, CNEr-1.36.0, coda-0.19-4, codetools-0.2-19, coloc-5.2.2, colorRamps-2.3.1, colorspace-2.1-0, colourpicker-1.2.0, combinat-0.0-8, commonmark-1.9.0, 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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. Homepage: https://bioconductor.org URL: https://bioconductor.org Extensions: abind-1.4-5, ade4-1.7-22, admisc-0.34, affxparser-1.74.0, affy-1.80.0, affycoretools-1.74.0, affyio-1.72.0, AgiMicroRna-2.52.0, agricolae-1.3-7, ALDEx2-1.34.0, AlgDesign-1.2.1, ALL-1.44.0, annaffy-1.74.0, annotate-1.80.0, AnnotationDbi-1.64.1, AnnotationFilter-1.26.0, AnnotationForge-1.44.0, AnnotationHub-3.10.0, anytime-0.3.9, aod-1.3.3, ape-5.7-1, aroma.affymetrix-3.2.1, aroma.apd-0.7.0, aroma.core-3.3.0, aroma.light-3.32.0, ash-1.0-15, askpass-1.2.0, assertthat-0.2.1, ATACseqQC-1.26.0, aws-2.5-3, aws.s3-0.3.21, aws.signature-0.6.0, awsMethods-1.1-1, backports-1.4.1, ballgown-2.34.0, base64-2.0.1, base64enc-0.1-3, basilisk-1.14.1, basilisk.utils-1.14.1, batchelor-1.18.1, baySeq-2.36.0, BBmisc-1.13, beachmat-2.18.0, beanplot-1.3.1, beeswarm-0.4.0, BH-1.81.0-1, BiasedUrn-2.0.11, Biobase-2.62.0, BiocBaseUtils-1.4.0, BiocFileCache-2.10.1, BiocGenerics-0.48.1, BiocIO-1.12.0, BiocManager-1.30.22, BiocNeighbors-1.20.2, BiocParallel-1.36.0, BiocSingular-1.18.0, BiocStyle-2.30.0, BiocVersion-3.18.1, biomaRt-2.58.0, biomformat-1.30.0, Biostrings-2.70.1, biovizBase-1.50.0, bit-4.0.5, bit64-4.0.5, bitops-1.0-7, blme-1.0-5, blob-1.2.4, bluster-1.12.0, bookdown-0.37, boot-1.3-28.1, brio-1.1.4, broom-1.0.5, broom.helpers-1.14.0, BSgenome-1.70.1, BSgenome.Cfamiliaris.UCSC.canFam3-1.4.0, BSgenome.Hsapiens.UCSC.hg19-1.4.3, BSgenome.Hsapiens.UCSC.hg38-1.4.5, BSgenome.Mmusculus.UCSC.mm10-1.4.3, bslib-0.6.1, bumphunter-1.44.0, ca-0.71.1, cachem-1.0.8, Cairo-1.6-2, calibrate-1.7.7, callr-3.7.3, CAMERA-1.58.0, car-3.1-2, carData-3.0-5, caret-6.0-94, Category-2.68.0, caTools-1.18.2, ccdata-1.28.0, ccmap-1.28.0, cellranger-1.1.0, CGHbase-1.62.0, checkmate-2.3.1, ChIPpeakAnno-3.36.0, circlize-0.4.15, class-7.3-22, classInt-0.4-10, cli-3.6.2, clipr-0.8.0, clock-0.7.0, clue-0.3-65, cluster-2.1.6, CNEr-1.38.0, coda-0.19-4, codetools-0.2-19, coloc-5.2.3, colorRamps-2.3.1, colorspace-2.1-0, colourpicker-1.3.0, combinat-0.0-8, commonmark-1.9.0, ComplexHeatmap-2.18.0, ConsensusClusterPlus-1.66.0, conumee-1.36.0, corpcor-1.6.10, corrplot-0.92, cowplot-1.1.2, cpp11-0.4.7, crayon-1.5.2, crossmeta-1.28.0, crosstalk-1.2.1, cummeRbund-2.44.0, curl-5.2.0, cytolib-2.14.0, CytoML-2.14.0, dada2-1.30.0, data.table-1.14.10, DBI-1.2.0, dbplyr-2.4.0, DeconRNASeq-1.44.0, DEGseq-1.56.1, DelayedArray-0.28.0, DelayedMatrixStats-1.24.0, deldir-2.0-2, dendextend-1.17.1, densvis-1.12.0, DEoptimR-1.1-3, derfinder-1.36.0, derfinderHelper-1.36.0, desc-1.4.3, DESeq2-1.42.0, deSolve-1.40, diagram-1.6.5, dichromat-2.0-0.1, diffcyt-1.22.0, diffobj-0.3.5, digest-0.6.33, diptest-0.77-0, dir.expiry-1.10.0, directlabels-2023.8.25, DirichletMultinomial-1.44.0, DNAcopy-1.76.0, docopt-0.7.1, doParallel-1.0.17, doRNG-1.8.6, dotCall64-1.1-1, dplyr-1.1.4, dqrng-0.3.2, DRIMSeq-1.30.0, DropletUtils-1.22.0, DT-0.31, dupRadar-1.32.0, DynDoc-1.80.0, e1071-1.7-14, EBImage-4.44.0, edgeR-4.0.6, egg-0.4.5, ellipse-0.5.0, ellipsis-0.3.2, emmeans-1.9.0, EnsDb.Hsapiens.v75-2.99.0, EnsDb.Hsapiens.v86-2.99.0, ensembldb-2.26.0, EnvStats-2.8.1, estimability-1.4.1, evaluate-0.23, ExperimentHub-2.10.0, extraDistr-1.10.0, fANCOVA-0.6-1, fansi-1.0.6, farver-2.1.1, fastcluster-1.2.3, fastDummies-1.7.3, fastICA-1.2-4, fastmap-1.1.1, fastmatch-1.1-4, fda-6.1.4, FDb.InfiniumMethylation.hg19-2.2.0, fdrtool-1.2.17, fds-1.8, ff-4.0.9, fftwtools-0.9-11, fgsea-1.28.0, filelock-1.0.3, fitdistrplus-1.1-11, flexmix-2.3-19, flowClust-3.40.0, flowCore-2.14.0, FlowSOM-2.10.0, FlowSorted.Blood.EPIC-2.6.0, FlowSorted.CordBloodCombined.450k-1.18.0, flowStats-4.14.0, flowViz-1.66.0, flowWorkspace-4.14.1, FNN-1.1.3.2, fontawesome-0.5.2, forcats-1.0.0, foreach-1.5.2, foreign-0.8-86, formatR-1.14, Formula-1.2-5, formula.tools-1.7.1, fpc-2.2-11, FRASER-1.14.0, fresh-0.2.0, fs-1.6.3, futile.logger-1.4.3, futile.options-1.0.1, future-1.33.1, future.apply-1.11.1, gbm-2.1.8.1, gclus-1.3.2, gcrma-2.74.0, gdata-3.0.0, gdsfmt-1.38.0, genefilter-1.84.0, geneLenDataBase-1.38.0, geneplotter-1.80.0, generics-0.1.3, GENESIS-2.32.0, GENIE3-1.24.0, GenomeInfoDb-1.38.5, GenomeInfoDbData-1.2.11, GenomicAlignments-1.38.1, GenomicFeatures-1.54.1, GenomicFiles-1.38.0, GenomicRanges-1.54.1, GenomicScores-2.14.3, GEOquery-2.70.0, GetoptLong-1.0.5, GGally-2.2.0, ggbeeswarm-0.7.2, ggbio-1.50.0, ggcyto-1.30.0, ggdendro-0.1.23, ggforce-0.4.1, ggnewscale-0.4.9, ggplot2-3.4.4, ggpointdensity-0.1.0, ggpubr-0.6.0, ggrastr-1.0.2, ggrepel-0.9.4, ggridges-0.5.5, ggsci-3.0.0, ggseqlogo-0.1, ggsignif-0.6.4, ggstats-0.5.1, ggthemes-5.0.0, ggvis-0.4.8, GLAD-2.66.0, Glimma-2.12.0, glmmTMB-1.1.8, glmnet-4.1-8, GlobalAncova-4.20.0, GlobalOptions-0.1.2, globals-0.16.2, globaltest-5.56.0, glue-1.7.0, GO.db-3.18.0, goftest-1.2-3, goseq-1.54.0, GOstats-2.68.0, gower-1.0.1, gplots-3.1.3, graph-1.80.0, gridExtra-2.3, GSA-1.03.2, GSEABase-1.64.0, gsl-2.1-8, gsmoothr-0.1.7, GSVA-1.50.0, gtable-0.3.4, gtools-3.9.5, Gviz-1.46.1, GWASExactHW-1.01, GWASTools-1.48.0, hardhat-1.3.0, haven-2.5.4, HDF5Array-1.30.0, hdrcde-3.4, heatmaply-1.5.0, here-1.0.1, hexbin-1.28.3, hgu133plus2.db-3.13.0, highr-0.10, Hmisc-5.1-1, HMMcopy-1.44.0, hms-1.1.3, Homo.sapiens-1.3.1, htmlTable-2.4.2, htmltools-0.5.7, htmlwidgets-1.6.4, httpuv-1.6.13, httr-1.4.7, hwriter-1.3.2.1, ica-1.0-3, IDPmisc-1.1.20, igraph-1.6.0, IHW-1.30.0, IlluminaHumanMethylation450kanno.ilmn12.hg19-0.6.1, IlluminaHumanMethylation450kmanifest-0.4.0, IlluminaHumanMethylationEPICanno.ilm10b2.hg19-0.6.0, IlluminaHumanMethylationEPICanno.ilm10b4.hg19-0.6.0, IlluminaHumanMethylationEPICmanifest-0.3.0, illuminaio-0.44.0, impute-1.76.0, InteractionSet-1.30.0, interactiveDisplayBase-1.40.0, interp-1.1-5, ipred-0.9-14, IRanges-2.36.0, irlba-2.3.5.1, isoband-0.2.7, isva-1.9, iterators-1.0.14, itertools-0.1-3, JADE-2.0-4, jomo-2.7-6, jpeg-0.1-10, jquerylib-0.1.4, jsonlite-1.8.8, KEGG.db-3.2.4, KEGGgraph-1.62.0, KEGGREST-1.42.0, kernlab-0.9-32, KernSmooth-2.23-22, klaR-1.7-3, knitr-1.45, ks-1.14.1, labeling-0.4.3, labelled-2.12.0, lambda.r-1.2.4, LaplacesDemon-16.1.6, later-1.3.2, lattice-0.22-5, latticeExtra-0.6-30, lava-1.7.3, lazyeval-0.2.2, LEA-3.14.0, leiden-0.4.3.1, lifecycle-1.0.4, limma-3.58.1, limSolve-1.5.7, listenv-0.9.0, lme4-1.1-35.1, lmerTest-3.1-3, lmtest-0.9-40, locfit-1.5-9.8, logistf-1.26.0, logspline-2.1.21, lpSolve-5.6.20, lpsymphony-1.30.0, lsa-0.73.3, lubridate-1.9.3, lumi-2.54.0, magrittr-2.0.3, MALDIquant-1.22.1, markdown-1.12, marray-1.80.0, maSigPro-1.74.0, MASS-7.3-60, MassSpecWavelet-1.68.0, mathjaxr-1.6-0, Matrix-1.6-4, MatrixGenerics-1.14.0, MatrixModels-0.5-3, matrixStats-1.2.0, mclust-6.0.1, MEDIPS-1.54.0, memoise-2.0.1, MetaboCoreUtils-1.10.0, metagenomeSeq-1.43.0, metaMA-3.1.3, metap-1.9, metapod-1.10.1, MethylSeekR-1.42.0, methylumi-2.48.0, Mfuzz-2.62.0, mgcv-1.9-1, mhsmm-0.4.21, mice-3.16.0, mime-0.12, minfi-1.48.0, miniUI-0.1.1.1, minqa-1.2.6, misc3d-0.9-1, missForest-1.5, missMethyl-1.36.0, mitml-0.4-5, mixOmics-6.26.0, mixsqp-0.3-54, mixtools-2.0.0, mlbench-2.1-3.1, MLInterfaces-1.82.0, mnormt-2.1.1, ModelMetrics-1.2.2.2, modeltools-0.2-23, MotifDb-1.44.0, motifmatchr-1.24.0, motifStack-1.46.0, MsCoreUtils-1.14.1, MsExperiment-1.4.0, MsFeatures-1.10.0, MSnbase-2.28.1, multcomp-1.4-25, MultiAssayExperiment-1.28.0, multicool-1.0.0, MultiDataSet-1.30.0, multtest-2.58.0, munsell-0.5.0, muscat-1.16.0, mutoss-0.1-13, mvtnorm-1.2-4, mzID-1.40.0, mzR-2.36.0, NADA-1.6-1.1, ncdf4-1.22, ncdfFlow-2.48.0, NCmisc-1.2.0, nleqslv-3.3.5, nlme-3.1-164, nloptr-2.0.3, nnet-7.3-19, NOISeq-2.46.0, nor1mix-1.3-2, nortest-1.0-4, numDeriv-2016.8-1.1, oligo-1.66.0, oligoClasses-1.64.0, ontologyIndex-2.11, openCyto-2.14.0, openssl-2.1.1, openxlsx-4.2.5.2, operator.tools-1.6.3, ordinal-2023.12-4, org.Hs.eg.db-3.18.0, org.Mm.eg.db-3.18.0, org.Rn.eg.db-3.18.0, OrganismDbi-1.44.0, OUTRIDER-1.20.0, pan-1.9, parallelly-1.36.0, patchwork-1.2.0, pbapply-1.7-2, pbkrtest-0.5.2, pcaMethods-1.94.0, pcaPP-2.0-4, perm-1.0-0.4, permute-0.9-7, PFAM.db-3.18.0, pheatmap-1.0.12, phyloseq-1.46.0, pillar-1.9.0, pixmap-0.4-12, pkgbuild-1.4.3, pkgconfig-2.0.3, pkgload-1.3.3, plogr-0.2.0, plot3D-1.4, plotly-4.10.3, plotrix-3.8-4, pls-2.8-3, plyr-1.8.9, pmp-1.14.0, png-0.1-8, polyclip-1.10-6, polyester-1.38.0, polynom-1.4-1, poweRlaw-0.70.6, prabclus-2.3-3, pracma-2.4.4, praise-1.0.0, preprocessCore-1.64.0, preseqR-4.0.0, prettyunits-1.2.0, pROC-1.18.5, processx-3.8.3, prodlim-2023.08.28, progress-1.2.3, progressr-0.14.0, pRoloc-1.42.0, pRolocdata-1.40.0, pRolocGUI-2.12.0, promises-1.2.1, ProtGenerics-1.34.0, proxy-0.4-27, PRROC-1.3.1, ps-1.7.5, PSCBS-0.66.0, PureCN-2.8.1, purrr-1.0.2, qap-0.1-2, QFeatures-1.12.0, qlcMatrix-0.9.7, qqconf-1.3.2, qqman-0.1.9, quadprog-1.5-8, quantreg-5.97, quantsmooth-1.68.0, questionr-0.7.8, qvalue-2.34.0, R.cache-0.16.0, R.devices-2.17.1, R.filesets-2.15.0, R.huge-0.10.0, R.methodsS3-1.8.2, R.oo-1.25.0, R.rsp-0.45.0, R.utils-2.12.3, R6-2.5.1, ragg-1.2.7, rainbow-3.7, randomcoloR-1.1.0.1, randomForest-4.7-1.1, RANN-2.6.1, rappdirs-0.3.3, rARPACK-0.11-0, RBGL-1.78.0, rbibutils-2.2.16, RColorBrewer-1.1-3, Rcpp-1.0.12, RcppAnnoy-0.0.21, RcppArmadillo-0.12.6.6.1, RcppEigen-0.3.3.9.4, RcppGSL-0.3.13, RcppHNSW-0.5.0, RcppML-0.3.7, RcppParallel-5.1.7, RcppProgress-0.4.2, RcppRoll-0.3.0, RcppTOML-0.2.2, RcppZiggurat-0.1.6, RCurl-1.98-1.14, Rdpack-2.6, reader-1.0.6, readr-2.1.4, readxl-1.4.3, recipes-1.0.9, regioneR-1.34.0, registry-0.5-1, remaCor-0.0.16, rematch-2.0.0, rematch2-2.1.2, Repitools-1.48.0, ReportingTools-2.42.3, reshape-0.8.9, reshape2-1.4.4, ResidualMatrix-1.12.0, restfulr-0.0.15, reticulate-1.34.0, Rfast-2.1.0, rGADEM-2.50.0, Rgraphviz-2.46.0, rhdf5-2.46.1, rhdf5filters-1.14.1, Rhdf5lib-1.24.1, RhpcBLASctl-0.23-42, Rhtslib-2.4.0, Ringo-1.66.0, rjson-0.2.21, rlang-1.1.3, rmarkdown-2.25, RNASeqPower-1.42.0, rngtools-1.5.2, robustbase-0.99-1, ROC-1.78.0, ROCR-1.0-11, rols-2.30.0, ropls-1.34.0, rpart-4.1.23, rprojroot-2.0.4, RProtoBufLib-2.14.0, rrcov-1.7-4, Rsamtools-2.18.0, Rsolnp-1.16, RSpectra-0.16-1, RSQLite-2.3.4, rstatix-0.7.2, rstudioapi-0.15.0, Rsubread-2.16.0, rsvd-1.0.5, rtracklayer-1.62.0, Rtsne-0.17, ruv-0.9.7.1, S4Arrays-1.2.0, S4Vectors-0.40.2, sampling-2.10, samr-3.0, sandwich-3.1-0, sass-0.4.8, SC3-1.30.0, ScaledMatrix-1.10.0, scales-1.3.0, SCANVIS-1.16.0, scater-1.30.1, scattermore-1.2, scran-1.30.0, scrime-1.3.5, sctransform-0.4.1, scuttle-1.12.0, segmented-2.0-1, SeqArray-1.42.0, seqLogo-1.68.0, SeqVarTools-1.40.0, seriation-1.5.4, Seurat-5.0.1, SeuratObject-5.0.1, sfsmisc-1.1-16, shape-1.4.6, shiny-1.8.0, shinyBS-0.61.1, shinydashboard-0.7.2, shinydashboardPlus-2.0.3, shinyFiles-0.9.3, shinyhelper-0.3.2, shinyjs-2.1.0, shinypanel-0.1.5, shinyWidgets-0.8.1, ShortRead-1.60.0, siggenes-1.76.0, Signac-1.12.0, SingleCellExperiment-1.24.0, SingleR-2.4.1, sitmo-2.0.2, slam-0.1-50, SMVar-1.3.4, sn-2.1.1, snow-0.4-4, SnowballC-0.7.1, SNPRelate-1.36.0, snpStats-1.52.0, sourcetools-0.1.7-1, sp-2.1-2, spam-2.10-0, SparseArray-1.2.3, SparseM-1.81, sparseMatrixStats-1.14.0, sparsesvd-0.2-2, spatstat.data-3.0-3, spatstat.explore-3.2-5, spatstat.geom-3.2-7, spatstat.random-3.2-2, spatstat.sparse-3.0-3, spatstat.utils-3.0-4, Spectra-1.12.0, SPIA-2.54.0, splitstackshape-1.4.8, SQUAREM-2021.1, stageR-1.24.0, statmod-1.5.0, stringi-1.8.3, stringr-1.5.1, struct-1.14.0, structToolbox-1.14.0, styler-1.10.2, SummarizedExperiment-1.32.0, survival-3.5-7, susieR-0.12.35, sva-3.50.0, sys-3.4.2, systemfonts-1.0.5, tensor-1.5, testthat-3.2.1, textshaping-0.3.7, TFBSTools-1.40.0, TFisher-0.2.0, TFMPvalue-0.0.9, TH.data-1.1-2, threejs-0.3.3, tibble-3.2.1, tidyr-1.3.0, tidyselect-1.2.0, tiff-0.1-12, timechange-0.2.0, timeDate-4032.109, tinytex-0.49, tkWidgets-1.80.0, TMB-1.9.10, truncnorm-1.0-9, TSP-1.2-4, tweenr-2.0.2, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, TxDb.Mmusculus.UCSC.mm10.knownGene-3.10.0, tximport-1.30.0, tzdb-0.4.0, ucminf-1.2.1, utf8-1.2.4, uwot-0.1.16, V8-4.4.1, variancePartition-1.32.2, VariantAnnotation-1.48.1, vctrs-0.6.5, vegan-2.6-4, venn-1.12, VennDiagram-1.7.3, VGAM-1.1-9, vipor-0.4.7, viridis-0.6.4, viridisLite-0.4.2, vroom-1.6.5, vsn-3.70.0, waiter-0.2.5, waldo-0.5.2, wateRmelon-2.8.0, webshot-0.5.5, widgetTools-1.80.0, withr-2.5.2, Wrench-1.20.0, WriteXLS-6.5.0, xcms-4.0.1, xfun-0.41, xgboost-1.7.6.1, XML-3.99-0.16, xml2-1.3.6, xtable-1.8-4, XVector-0.42.0, yaml-2.3.8, zCompositions-1.5.0-1, zip-2.3.0, zlibbioc-1.48.0, zoo-1.8-12 Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://sourceforge.net/projects/weinberg-r2r/files/latest/download/ r2r]
| align="center" | [https://sourceforge.net/projects/weinberg-r2r/files/latest/download/ r2r]
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| align="center" | [https://github.com/HOST-Oman/libraqm raqm]
| align="center" | [https://github.com/HOST-Oman/libraqm raqm]
| align="center" | -
| align="center" | -
| align="center" | 0.9.0
| align="center" | 0.9.0, 0.10.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Raqm is a small library that encapsulates the logic for complex text layout and provides a convenient API. Homepage: https://github.com/HOST-Oman/libraqm URL: https://github.com/HOST-Oman/libraqm<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Raqm is a small library that encapsulates the logic for complex text layout and provides a convenient API. Homepage: https://github.com/HOST-Oman/libraqm URL: https://github.com/HOST-Oman/libraqm<br /><br /><br /></div>
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| align="center" | [https://github.com/amkozlov/raxml-ng raxml-ng]
| align="center" | [https://github.com/amkozlov/raxml-ng raxml-ng]
| align="center" | -
| align="center" | -
| align="center" | 0.9.0, 1.0.1
| align="center" | 0.9.0, 1.0.1, 1.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Homepage: https://github.com/amkozlov/raxml-ng URL: https://github.com/amkozlov/raxml-ng<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Homepage: https://github.com/amkozlov/raxml-ng URL: https://github.com/amkozlov/raxml-ng<br /><br /><br /></div>
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| align="center" | [http://www.rdkit.org/ rdkit]
| align="center" | [http://www.rdkit.org/ rdkit]
| align="center" | chem
| align="center" | chem
| align="center" | 2018.03.3, 2019.03.4, 2020.09.1b1, 2021.03.3, 2021.09.3, 2021.09.4, 2022.09.4
| align="center" | 2018.03.3, 2019.03.4, 2020.09.1b1, 2021.03.3, 2021.09.3, 2021.09.4, 2022.09.4, 2023.09.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Homepage: http://www.rdkit.org/ URL: http://www.rdkit.org/ Compatible modules: python/3.5.4 (default), python/3.6.3, python/3.7.4 Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Homepage: http://www.rdkit.org/ URL: http://www.rdkit.org/ Compatible modules: python/3.10, python/3.11 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://re2c.org/ re2c]
| align="center" | [https://re2c.org/ re2c]
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| align="center" | bio
| align="center" | bio
| align="center" | 1.08
| align="center" | 1.08
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes. Homepage: http://eddylab.org/software/recon/ URL: http://eddylab.org/software/recon/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes. Homepage: http://eddylab.org/software/recon/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/rlabduke/reduce reduce]
| align="center" | [https://github.com/rlabduke/reduce reduce]
| align="center" | -
| align="center" | -
| align="center" | 4.14, 20180820
| align="center" | 4.14, 20180820
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Reduce - tool for adding and correcting hydrogens in PDB files Homepage: https://github.com/rlabduke/reduce URL: https://github.com/rlabduke/reduce<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Reduce - tool for adding and correcting hydrogens in PDB files Homepage: https://github.com/rlabduke/reduce<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/eth-cscs/reframe reframe]
| align="center" | [https://github.com/eth-cscs/reframe reframe]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center. The method has the following properties It works on quantitative and binary traits, including binary traits with unbalanced case-control ratios It can process multiple phenotypes at once For binary traits it supports Firth logistic regression and an SPA test It can perform gene/region-based burden tests It is fast and memory efficient It supports the BGEN, PLINK bed/bim/fam and PLINK2 pgen/pvar/psam genetic data formats It is ideally suited for implementation in Apache Spark (see GLOW) Citation Mbatchou, J., Barnard, L., Backman, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat Genet 53, 10971103 (2021). https://doi.org/10.1038/s41588-021-00870-7 Homepage: https://rgcgithub.github.io/regenie/ URL: https://rgcgithub.github.io/regenie/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center. The method has the following properties It works on quantitative and binary traits, including binary traits with unbalanced case-control ratios It can process multiple phenotypes at once For binary traits it supports Firth logistic regression and an SPA test It can perform gene/region-based burden tests It is fast and memory efficient It supports the BGEN, PLINK bed/bim/fam and PLINK2 pgen/pvar/psam genetic data formats It is ideally suited for implementation in Apache Spark (see GLOW) Citation Mbatchou, J., Barnard, L., Backman, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat Genet 53, 10971103 (2021). https://doi.org/10.1038/s41588-021-00870-7 Homepage: https://rgcgithub.github.io/regenie/ URL: https://rgcgithub.github.io/regenie/<br /><br /><br /></div>
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|-
| align="center" | [https://bitbucket.org/scheres/relion-3.0_beta.git relion]
| align="center" | [https://www3.mrc-lmb.cam.ac.uk/relion/ relion]
| align="center" | chem
| align="center" | chem
| align="center" | 2.1.0, 3.0, 3.1.1, 4.0.0
| align="center" | 2.1.0, 3.0, 3.1.1, 4.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Homepage: https://bitbucket.org/scheres/relion-3.0_beta.git URL: https://bitbucket.org/scheres/relion-3.0_beta.git Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Homepage: https://www3.mrc-lmb.cam.ac.uk/relion/ URL: https://www3.mrc-lmb.cam.ac.uk/relion/ Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/TACC/remora remora]
| align="center" | [https://github.com/TACC/remora remora]
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| align="center" | [https://repast.github.io/ repasthpc]
| align="center" | [https://repast.github.io/ repasthpc]
| align="center" | bio
| align="center" | bio
| align="center" | 2.2.0, 2.3.0
| align="center" | 2.0, 2.2.0, 2.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. Homepage: https://repast.github.io/ URL: https://repast.github.io/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. Homepage: https://repast.github.io/ URL: https://repast.github.io/ Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://github.com/ospray/rkcommon rkcommon]
| align="center" | [https://github.com/ospray/rkcommon rkcommon]
| align="center" | -
| align="center" | -
| align="center" | 1.4.2, 1.10.0
| align="center" | 1.4.2, 1.10.0, 1.11.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel RenderKit common library Homepage: https://github.com/ospray/rkcommon URL: https://github.com/ospray/rkcommon<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel RenderKit common library Homepage: https://github.com/ospray/rkcommon URL: https://github.com/ospray/rkcommon<br /><br /><br /></div>
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| align="center" | [https://root.cern.ch/drupal/ root]
| align="center" | [https://root.cern.ch/drupal/ root]
| align="center" | tools
| align="center" | tools
| align="center" | 5.34.36, 6.08.02, 6.14.04, 6.20.04, 6.24.06, 6.26.06
| align="center" | 5.34.36, 6.08.02, 6.14.04, 6.20.04, 6.24.06, 6.26.06, 6.28.06
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Homepage: https://root.cern.ch/drupal/ URL: https://root.cern.ch/drupal/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. Homepage: https://root.cern.ch/drupal/ URL: https://root.cern.ch/drupal/ Keyword:tools<br /><br /><br /></div>
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| align="center" | chem
| align="center" | chem
| align="center" | 3.9, 3.10, 3.12, 3.13, 2019.21.60746
| align="center" | 3.9, 3.10, 3.12, 3.13, 2019.21.60746
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. This is a weekly release. Homepage: https://www.rosettacommons.org URL: https://www.rosettacommons.org Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. This is a weekly release. Homepage: https://www.rosettacommons.org Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [http://deweylab.github.io/RSEM/ rsem]
| align="center" | [http://deweylab.github.io/RSEM/ rsem]
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| align="center" | [https://www.ruby-lang.org ruby]
| align="center" | [https://www.ruby-lang.org ruby]
| align="center" | tools
| align="center" | tools
| align="center" | 2.3.1, 2.6.1, 2.7.1
| align="center" | 2.3.1, 2.6.1, 2.7.1, 3.2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. Homepage: https://www.ruby-lang.org URL: https://www.ruby-lang.org Extensions: activesupport-5.2.4.2, addressable-2.7.0, arr-pm-0.0.10, backports-3.17.0, bundler-2.1.4, cabin-0.9.0, childprocess-3.0.0, clamp-1.3.1, concurrent-ruby-1.1.6, connection_pool-2.2.2, diff-lcs-1.3, ethon-0.12.0, faraday-0.17.3, faraday_middleware-0.14.0, ffi-1.12.2, gh-0.16.0, highline-2.0.3, i18n-1.8.2, json-2.2.0, launchy-2.5.0, minitest-5.14.0, multi_json-1.14.1, multipart-post-1.2.0, mustermann-1.1.1, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-4.0.3, pusher-client-0.6.2, rack-2.2.2, rack-protection-2.0.8.1, rack-test-1.1.0, rspec-3.9.0, rspec-core-3.9.1, rspec-expectations-3.9.1, rspec-mocks-3.9.1, rspec-support-3.9.2, ruby2_keywords-0.0.2, sinatra-2.0.8.1, thread_safe-0.3.6, tilt-2.0.10, typhoeus-1.3.1, tzinfo-1.2.7, websocket-1.2.8 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. Homepage: https://www.ruby-lang.org URL: https://www.ruby-lang.org Extensions: activesupport-5.2.8.1, addressable-2.8.4, arr-pm-0.0.12, backports-3.24.1, bundler-2.4.14, cabin-0.9.0, childprocess-4.1.0, clamp-1.3.2, concurrent-ruby-1.2.2, connection_pool-2.4.1, diff-lcs-1.5.0, ethon-0.16.0, faraday-1.2.0, faraday-net_http-3.0.2, faraday_middleware-1.2.0, ffi-1.15.5, gh-0.18.0, highline-2.1.0, i18n-1.14.1, json-2.6.3, launchy-2.5.2, minitest-5.18.0, multi_json-1.15.0, multipart-post-2.3.0, mustermann-3.0.0, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-5.0.1, pusher-client-0.6.2, rack-2.2.4, rack-protection-3.0.6, rack-test-2.1.0, rspec-3.12.0, rspec-core-3.12.2, rspec-expectations-3.12.3, rspec-mocks-3.12.5, rspec-support-3.12.0, ruby2_keywords-0.0.5, sinatra-3.0.6, thread_safe-0.3.6, tilt-2.2.0, typhoeus-1.4.0, tzinfo-1.1.0, websocket-1.2.9, zeitwerk-2.6.8 Keyword:tools<br /><br /><br /></div>
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|-
| align="center" | [https://rubygems.org rubygems]
| align="center" | [https://rubygems.org rubygems]
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| align="center" | [https://www.rust-lang.org rust]
| align="center" | [https://www.rust-lang.org rust]
| align="center" | tools
| align="center" | tools
| align="center" | 1.28.0, 1.41.0, 1.47.0, 1.53.0, 1.59.0, 1.65.0, 1.70.0
| align="center" | 1.28.0, 1.41.0, 1.47.0, 1.53.0, 1.59.0, 1.65.0, 1.70.0, 1.76.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://www.rust-lang.org URL: https://www.rust-lang.org Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. Homepage: https://www.rust-lang.org URL: https://www.rust-lang.org Keyword:tools<br /><br /><br /></div>
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| align="center" | [https://github.com/COMBINE-lab/salmon salmon]
| align="center" | [https://github.com/COMBINE-lab/salmon salmon]
| align="center" | bio
| align="center" | bio
| align="center" | 0.11.3, 0.12.0, 0.14.0, 0.14.2-1, 1.1.0, 1.3.0, 1.4.0
| align="center" | 0.11.3, 0.12.0, 0.14.0, 0.14.2-1, 1.1.0, 1.3.0, 1.4.0, 1.10.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon URL: https://github.com/COMBINE-lab/salmon Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon URL: https://github.com/COMBINE-lab/salmon Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://www.htslib.org/ samtools]
| align="center" | [https://www.htslib.org/ samtools]
| align="center" | bio
| align="center" | bio
| align="center" | 0.1.20, 1.3.1, 1.9, 1.10, 1.11, 1.12, 1.13, 1.15.1, 1.16.1, 1.17
| align="center" | 0.1.20, 1.3.1, 1.9, 1.10, 1.11, 1.12, 1.13, 1.15.1, 1.16.1, 1.17, 1.18
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div>
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| align="center" | 2.5
| align="center" | 2.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes. Homepage: https://www.scalasca.org/ URL: https://www.scalasca.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes. Homepage: https://www.scalasca.org/ URL: https://www.scalasca.org/<br /><br /><br /></div>
|-
| align="center" | [https://scipopt.org/ scipoptsuite]
| align="center" | -
| align="center" | 9.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a framework for constraint integer programming and branch-cut-and-price. It allows for total control of the solution process and the access of detailed information down to the guts of the solver. Homepage: https://scipopt.org/ URL: https://scipopt.org/ Compatible modules: python/3.10, python/3.11 Extensions: PySCIPOpt-5.0.0<br /><br /><br /></div>
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|-
| align="center" | [http://python.org/ scipy-stack]
| align="center" | [http://python.org/ scipy-stack]
| align="center" | math
| align="center" | math
| align="center" | 2017b, 2018b, 2019a, 2019b, 2020a, 2020b, 2021a, 2022a, 2023a, 2023b
| align="center" | 2017b, 2018b, 2019a, 2019b, 2020a, 2020b, 2021a, 2022a, 2023a, 2023b
| Documentation: [[Python]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11 Extensions: anyio-3.6.2, arff-0.9, argon2_cffi-21.3.0, argon2_cffi_bindings-21.2.0, async_generator-1.10, attrs-22.2.0, backports-abc-0.5, backports.shutil_get_terminal_size-1.0.0, bcrypt-4.0.1, beautifulsoup4-4.11.2, bitstring-4.0.1, bleach-6.0.0, certifi-2022.12.7, cffi-1.15.1, chardet-5.1.0, charset_normalizer-3.0.1, contourpy-1.0.7, cryptography-39.0.1, cycler-0.11.0, Cython-0.29.33, deap-1.3.3, defusedxml-0.7.1, dnspython-2.3.0, ecdsa-0.18.0, entrypoints-0.4, fastjsonschema-2.16.2, fonttools-4.38.0, funcsigs-1.0.2, idna-3.4, importlib_resources-5.12.0, ipywidgets-8.0.4, Jinja2-3.1.2, jsonschema-4.17.3, jupyter_events-0.6.3, jupyter_server-2.3.0, jupyter_server_terminals-0.4.4, jupyterlab_pygments-0.2.2, jupyterlab_widgets-3.0.5, kiwisolver-1.4.4, lockfile-0.12.2, MarkupSafe-2.1.2, matplotlib-3.7.0, mistune-2.0.5, mock-5.0.1, mpmath-1.2.1, nbclassic-0.5.2, nbclient-0.7.2, nbconvert-7.2.9, nbformat-5.7.3, netaddr-0.8.0, netifaces-0.11.0, nose-1.3.7, notebook-6.5.2, notebook_shim-0.2.2, numpy-1.24.2, pandas-1.5.3, pandocfilters-1.5.0, paramiko-3.0.0, path-16.6.0, path.py-12.5.0, pathlib2-2.3.7, paycheck-1.0.2, pbr-5.11.1, Pillow-9.4.0, pkgutil_resolve_name-1.3.10, prometheus_client-0.16.0, pycparser-2.21, PyNaCl-1.5.0, pyparsing-3.0.9, pyrsistent-0.19.3, python_json_logger-2.0.7, pytz-2022.7.1, PyYAML-6.0, requests-2.28.2, rfc3339_validator-0.1.4, rfc3986_validator-0.1.1, scipy-1.10.1, Send2Trash-1.8.0, simplegeneric-0.8.1, singledispatch-4.0.0, sniffio-1.3.0, soupsieve-2.4, sympy-1.11.1, terminado-0.17.1, testpath-0.6.0, tinycss2-1.2.1, typing_extensions-4.5.0, urllib3-1.26.14, webencodings-0.5.1, websocket_client-1.5.1, widgetsnbextension-4.0.5 Keyword:math<br /><br /><br /></div>
| Documentation: [[Python]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ URL: http://python.org/ Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: anyio-3.7.1, arff-0.9, argon2_cffi-23.1.0, argon2_cffi_bindings-21.2.0, async_generator-1.10, attrs-23.1.0, backports-abc-0.5, backports.shutil_get_terminal_size-1.0.0, bcrypt-4.0.1, beautifulsoup4-4.12.2, bitarray-2.8.1, bitstring-4.1.1, bleach-6.0.0, certifi-2023.7.22, cffi-1.15.1, chardet-5.2.0, charset_normalizer-3.2.0, contourpy-1.1.0, cryptography-39.0.1, cycler-0.11.0, Cython-0.29.36, deap-1.4.1, defusedxml-0.7.1, dnspython-2.4.2, ecdsa-0.18.0, entrypoints-0.4, fastjsonschema-2.18.0, fonttools-4.42.1, funcsigs-1.0.2, idna-3.4, importlib_resources-6.0.1, Jinja2-3.1.2, jsonschema-4.19.0, jsonschema_specifications-2023.7.1, kiwisolver-1.4.5, lockfile-0.12.2, MarkupSafe-2.1.3, matplotlib-3.7.2, mistune-3.0.1, mock-5.1.0, mpmath-1.3.0, netaddr-0.8.0, netifaces-0.11.0, nose-1.3.7, numpy-1.25.2, pandas-2.1.0, pandocfilters-1.5.0, paramiko-3.3.1, path-16.7.1, path.py-12.5.0, pathlib2-2.3.7.post1, paycheck-1.0.2, pbr-5.11.1, Pillow-10.0.0, pkgutil_resolve_name-1.3.10, prometheus_client-0.17.1, pycparser-2.21, PyNaCl-1.5.0, pyparsing-3.0.9, pyrsistent-0.19.3, python_json_logger-2.0.7, pytz-2023.3, PyYAML-6.0.1, referencing-0.30.2, requests-2.31.0, rfc3339_validator-0.1.4, rfc3986_validator-0.1.1, rpds_py-0.10.0, scipy-1.11.2, Send2Trash-1.8.2, simplegeneric-0.8.1, singledispatch-4.1.0, sniffio-1.3.0, soupsieve-2.4.1, sympy-1.12, terminado-0.17.1, testpath-0.6.0, tinycss2-1.2.1, typing_extensions-4.7.1, tzdata-2023.3, urllib3-2.0.4, webencodings-0.5.1, websocket_client-1.6.2 Keyword:math<br /><br /><br /></div>
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| align="center" | [https://www.score-p.org score-p]
| align="center" | [https://www.score-p.org score-p]
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| align="center" | [https://bioinf.shenwei.me/seqkit/ seqkit]
| align="center" | [https://bioinf.shenwei.me/seqkit/ seqkit]
| align="center" | -
| align="center" | -
| align="center" | 0.13.2, 0.15.0, 2.3.1
| align="center" | 0.13.2, 0.15.0, 2.3.1, 2.5.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This project describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OS X, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. Homepage: https://bioinf.shenwei.me/seqkit/ URL: https://bioinf.shenwei.me/seqkit/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. This project describes a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing. SeqKit provides executable binary files for all major operating systems, including Windows, Linux, and Mac OS X, and can be directly used without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. Homepage: https://bioinf.shenwei.me/seqkit/ URL: https://bioinf.shenwei.me/seqkit/<br /><br /><br /></div>
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| align="center" | phys
| align="center" | phys
| align="center" | 1.1.1, 1.5.0
| align="center" | 1.1.1, 1.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. Also installed is the 'thirdorder' package of Python scripts. Homepage: http://www.shengbte.org/ URL: http://www.shengbte.org/ Extensions: thirdorder-1.0.2 Keyword:phys<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. Also installed is the 'thirdorder' package of Python scripts. Homepage: http://www.shengbte.org/ URL: http://www.shengbte.org/ Extensions: thirdorder-1.1.1 Keyword:phys<br /><br /><br /></div>
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| align="center" | [http://compbio.cs.toronto.edu/shrimp/ shrimp]
| align="center" | [http://compbio.cs.toronto.edu/shrimp/ shrimp]
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| align="center" | bio
| align="center" | bio
| align="center" | 1.33
| align="center" | 1.33
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Windowed Adaptive Trimming for fastq files using quality Homepage: https://github.com/najoshi/sickle URL: https://github.com/najoshi/sickle Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Windowed Adaptive Trimming for fastq files using quality Homepage: https://github.com/najoshi/sickle Keyword:bio<br /><br /><br /></div>
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| align="center" | [http://departments.icmab.es/leem/siesta siesta]
| align="center" | [http://departments.icmab.es/leem/siesta siesta]
| align="center" | chem
| align="center" | chem
| align="center" | 4.1-MaX-3.0, 4.0.1, 4.1-b3, 4.1-b4, 4.1.5
| align="center" | 4.1-MaX-3.0, 4.0.1, 4.1-b3, 4.1-b4, 4.1.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. This version was built with Lua support. Homepage: http://departments.icmab.es/leem/siesta URL: http://departments.icmab.es/leem/siesta Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Homepage: http://departments.icmab.es/leem/siesta URL: http://departments.icmab.es/leem/siesta Keyword:chem<br /><br /><br /></div>
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| align="center" | [http://sift.bii.a-star.edu.sg/ sift4g]
| align="center" | [http://sift.bii.a-star.edu.sg/ sift4g]
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| align="center" | [https://slepc.upv.es/ slepc]
| align="center" | [https://slepc.upv.es/ slepc]
| align="center" | -
| align="center" | -
| align="center" | 3.10.2, 3.14.2, 3.17.2, 3.19.2
| align="center" | 3.10.2, 3.14.2, 3.17.2, 3.19.2, 3.20.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. Homepage: https://slepc.upv.es/ URL: https://slepc.upv.es/ Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: slepc4py-3.19.2<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. Homepage: https://slepc.upv.es/ URL: https://slepc.upv.es/ Compatible modules: python/3.11, python/3.10 Extensions: slepc4py-3.20.1<br /><br /><br /></div>
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| align="center" | [https://slepc.upv.es/ slepc-complex]
| align="center" | -
| align="center" | 3.20.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. Homepage: https://slepc.upv.es/ URL: https://slepc.upv.es/ Compatible modules: python/3.11, python/3.10 Extensions: slepc4py-3.20.1<br /><br /><br /></div>
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| align="center" | [https://www.slicer.org/ slicer]
| align="center" | [https://www.slicer.org/ slicer]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. Homepage: https://www.slicer.org/ URL: https://www.slicer.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. Homepage: https://www.slicer.org/ URL: https://www.slicer.org/<br /><br /><br /></div>
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| align="center" | [https://messerlab.org/slim/ slim]
| align="center" | [https://messerlab.org/slim slim]
| align="center" | -
| align="center" | -
| align="center" | 3.3.2, 3.4.0, 4.0.1
| align="center" | 3.3.2, 3.4.0, 4.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios. The underlying individual-based simulation engine is highly optimized to enable modeling of entire chromosomes in large populations. Homepage: https://messerlab.org/slim/ URL: https://messerlab.org/slim/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Homepage: https://messerlab.org/slim URL: https://messerlab.org/slim<br /><br /><br /></div>
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| align="center" | [https://github.com/ruanjue/smartdenovo smartdenovo]
| align="center" | [https://github.com/ruanjue/smartdenovo smartdenovo]
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| align="center" | [http://soci.sourceforge.net/ soci]
| align="center" | [http://soci.sourceforge.net/ soci]
| align="center" | -
| align="center" | -
| align="center" | 4.0.2
| align="center" | 4.0.2, 4.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. Homepage: http://soci.sourceforge.net/ URL: http://soci.sourceforge.net/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. Homepage: http://soci.sourceforge.net/ URL: http://soci.sourceforge.net/<br /><br /><br /></div>
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| align="center" | [https://github.com/gabime/spdlog spdlog]
| align="center" | [https://github.com/gabime/spdlog spdlog]
| align="center" | -
| align="center" | -
| align="center" | 1.9.2
| align="center" | 1.9.2, 1.11.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Very fast, header-only/compiled, C++ logging library. Homepage: https://github.com/gabime/spdlog URL: https://github.com/gabime/spdlog<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Very fast, header-only/compiled, C++ logging library. Homepage: https://github.com/gabime/spdlog URL: https://github.com/gabime/spdlog<br /><br /><br /></div>
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SpectrA stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. SpectrA is implemented as a header-only C++ library, whose only dependency, Eigen, is also header-only. Hence SpectrA can be easily embedded in C++ projects that require calculating eigenvalues of large matrices. Homepage: https://spectralib.org/index.html URL: https://spectralib.org/index.html<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SpectrA stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. SpectrA is implemented as a header-only C++ library, whose only dependency, Eigen, is also header-only. Hence SpectrA can be easily embedded in C++ projects that require calculating eigenvalues of large matrices. Homepage: https://spectralib.org/index.html URL: https://spectralib.org/index.html<br /><br /><br /></div>
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| align="center" | [https://github.com/atztogo/spglib spglib]
| align="center" | [https://github.com/spglib/spglib spglib]
| align="center" | chem
| align="center" | chem
| align="center" | 1.9.9, 1.16.0, 2.0.2
| align="center" | 1.9.9, 1.16.0, 2.0.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Spglib is a C library for finding and handling crystal symmetries. Homepage: https://github.com/atztogo/spglib URL: https://github.com/atztogo/spglib Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Spglib is a C library for finding and handling crystal symmetries. Homepage: https://github.com/spglib/spglib URL: https://github.com/spglib/spglib Keyword:chem<br /><br /><br /></div>
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| align="center" | [https://github.com/rvaser/spoa spoa]
| align="center" | [https://github.com/rvaser/spoa spoa]
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| align="center" | math
| align="center" | math
| align="center" | 5.0
| align="center" | 5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scalable Parallel Pseudo Random Number Generators Library Homepage: http://www.sprng.org/ URL: http://www.sprng.org/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scalable Parallel Pseudo Random Number Generators Library Homepage: http://www.sprng.org/ Keyword:math<br /><br /><br /></div>
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| align="center" | [https://www.sqlite.org/ sqlite]
| align="center" | [https://www.sqlite.org/ sqlite]
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| align="center" | [https://github.com/ncbi/sra-tools sra-toolkit]
| align="center" | [https://github.com/ncbi/sra-tools sra-toolkit]
| align="center" | bio
| align="center" | bio
| align="center" | 2.8.2-1, 2.9.6, 2.10.8, 3.0.0
| align="center" | 2.8.2-1, 2.9.6, 2.10.8, 3.0.0, 3.0.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format Homepage: https://github.com/ncbi/sra-tools URL: https://github.com/ncbi/sra-tools Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format Homepage: https://github.com/ncbi/sra-tools URL: https://github.com/ncbi/sra-tools Keyword:bio<br /><br /><br /></div>
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| align="center" | [https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library ssw]
| align="center" | [https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library ssw]
| align="center" | -
| align="center" | -
| align="center" | 1.1
| align="center" | 1.1, 1.2.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library URL: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library URL: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library<br /><br /><br /></div>
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| align="center" | [https://github.com/alexdobin/STAR star]
| align="center" | [https://github.com/alexdobin/STAR star]
| align="center" | bio
| align="center" | bio
| align="center" | 2.6.1c, 2.7.0a, 2.7.1a, 2.7.3a, 2.7.4a, 2.7.5a, 2.7.8a, 2.7.9a
| align="center" | 2.6.1c, 2.7.0a, 2.7.1a, 2.7.3a, 2.7.4a, 2.7.5a, 2.7.8a, 2.7.9a, 2.7.11a
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR URL: https://github.com/alexdobin/STAR Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. Homepage: https://github.com/alexdobin/STAR URL: https://github.com/alexdobin/STAR Keyword:bio<br /><br /><br /></div>
|-
|-
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| align="center" | [http://subread.sourceforge.net/ subread]
| align="center" | [http://subread.sourceforge.net/ subread]
| align="center" | bio
| align="center" | bio
| align="center" | 1.5.2, 1.6.4, 2.0.0, 2.0.3
| align="center" | 1.5.2, 1.6.4, 2.0.0, 2.0.3, 2.0.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: High performance read alignment, quantification and mutation discovery Homepage: http://subread.sourceforge.net/ URL: http://subread.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: High performance read alignment, quantification and mutation discovery Homepage: http://subread.sourceforge.net/ URL: http://subread.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://faculty.cse.tamu.edu/davis/suitesparse.html suitesparse]
| align="center" | [https://faculty.cse.tamu.edu/davis/suitesparse.html suitesparse]
| align="center" | math
| align="center" | math
| align="center" | 4.5.4, 5.4.0, 5.7.1, 5.10.1
| align="center" | 4.5.4, 5.4.0, 5.7.1, 5.10.1, 5.13.0, 7.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuiteSparse is a collection of libraries manipulate sparse matrices. Homepage: https://faculty.cse.tamu.edu/davis/suitesparse.html URL: https://faculty.cse.tamu.edu/davis/suitesparse.html Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuiteSparse is a collection of libraries to manipulate sparse matrices. Homepage: https://faculty.cse.tamu.edu/davis/suitesparse.html URL: https://faculty.cse.tamu.edu/davis/suitesparse.html Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [http://metabarcoding.org/sumatra sumaclust]
| align="center" | [http://metabarcoding.org/sumatra sumaclust]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eclipse Sumo is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large road networks. Homepage: https://github.com/eclipse/sumo/ URL: https://github.com/eclipse/sumo/ Compatible modules: python/3.8, python/3.9, python/3.10<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Eclipse Sumo is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large road networks. Homepage: https://github.com/eclipse/sumo/ URL: https://github.com/eclipse/sumo/ Compatible modules: python/3.8, python/3.9, python/3.10<br /><br /><br /></div>
|-
|-
| align="center" | [https://computation.llnl.gov/projects/sundials sundials]
| align="center" | [https://computing.llnl.gov/projects/sundials sundials]
| align="center" | -
| align="center" | -
| align="center" | 2.7.0, 4.1.0, 5.3.0, 5.7.0, 6.4.1
| align="center" | 2.7.0, 4.1.0, 5.3.0, 5.7.0, 6.4.1, 6.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: https://computation.llnl.gov/projects/sundials URL: https://computation.llnl.gov/projects/sundials<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: https://computing.llnl.gov/projects/sundials URL: https://computing.llnl.gov/projects/sundials<br /><br /><br /></div>
|-
|-
| align="center" | [http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ superlu]
| align="center" | [http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ superlu]
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| align="center" | 1.1.0
| align="center" | 1.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Structural variation and indel detection by local assembly Homepage: https://github.com/walaj/svaba URL: https://github.com/walaj/svaba<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Structural variation and indel detection by local assembly Homepage: https://github.com/walaj/svaba URL: https://github.com/walaj/svaba<br /><br /><br /></div>
|-
| align="center" | [https://swatplus.gitbook.io swat+]
| align="center" | -
| align="center" | 60.5.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Soil and Water Assessment Tool (SWAT) is a small watershed to river basin-scale model used to simulate the quality and quantity of surface and ground water and predict the environmental impact of land use, land management practices, and climate change. In order to face present and future challenges in water resources modeling SWAT code has undergone major modifications over the past few years, resulting in SWAT+, a completely revised version of the model. SWAT+ provides a more flexible spatial representation of interactions and processes within a watershed. Homepage: https://swatplus.gitbook.io URL: https://swatplus.gitbook.io<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.swi-prolog.org/ swi-prolog]
| align="center" | [https://www.swi-prolog.org/ swi-prolog]
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| align="center" | [http://www.swig.org/ swig]
| align="center" | [http://www.swig.org/ swig]
| align="center" | -
| align="center" | -
| align="center" | 3.0.12, 4.0.1, 4.0.2
| align="center" | 3.0.12, 4.0.1, 4.0.2, 4.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Homepage: http://www.swig.org/ URL: http://www.swig.org/ Compatible modules: python/2.7.14, python/3.5.4, python/3.6.3, python/3.7.4, python/3.8.0<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Homepage: http://www.swig.org/ URL: http://www.swig.org/<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/symengine/symengine symengine]
| align="center" | [https://github.com/symengine/symengine symengine]
| align="center" | -
| align="center" | -
| align="center" | 0.6.0, 0.8.1, 0.9.0, 0.10.1
| align="center" | 0.6.0, 0.8.1, 0.9.0, 0.10.1, 0.11.1, 0.11.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SymEngine is a standalone fast C++ symbolic manipulation library. Homepage: https://github.com/symengine/symengine URL: https://github.com/symengine/symengine Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: symengine-0.10.0<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SymEngine is a standalone fast C++ symbolic manipulation library. Homepage: https://github.com/symengine/symengine URL: https://github.com/symengine/symengine Compatible modules: python/3.10, python/3.11 Extensions: symengine-0.11.0<br /><br /><br /></div>
|-
|-
| align="center" | [http://samtools.sourceforge.net tabix]
| align="center" | [http://samtools.sourceforge.net tabix]
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| align="center" | 2.27.1, 2.30.1
| align="center" | 2.27.1, 2.30.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. Homepage: http://tau.uoregon.edu URL: http://tau.uoregon.edu Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. Homepage: http://tau.uoregon.edu URL: http://tau.uoregon.edu Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/dtarb/TauDEM/wiki taudem]
| align="center" | -
| align="center" | 5.3.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TauDEM (Terrain Analysis Using Digital Elevation Models) is a suite of Digital Elevation Model (DEM) tools for the extraction and analysis of hydrologic information from topography as represented by a DEM. Homepage: https://github.com/dtarb/TauDEM/wiki URL: https://github.com/dtarb/TauDEM/wiki<br /><br /><br /></div>
|-
|-
| align="center" | [https://bioinf.shenwei.me/taxonkit/ taxonkit]
| align="center" | [https://bioinf.shenwei.me/taxonkit/ taxonkit]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files for major operating systems including Windows, Linux, and Mac OS X, and can be directly used without any dependencies nor local database buiding. Homepage: https://bioinf.shenwei.me/taxonkit/ URL: https://bioinf.shenwei.me/taxonkit/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files for major operating systems including Windows, Linux, and Mac OS X, and can be directly used without any dependencies nor local database buiding. Homepage: https://bioinf.shenwei.me/taxonkit/ URL: https://bioinf.shenwei.me/taxonkit/<br /><br /><br /></div>
|-
|-
| align="center" | [http://software.intel.com/en-us/articles/intel-tbb/ tbb]
| align="center" | [https://github.com/oneapi-src/oneTBB tbb]
| align="center" | tools
| align="center" | tools
| align="center" | 2018_U5, 2017.2.132, 2020.2, 2021.8.0
| align="center" | 2018_U5, 2017.2.132, 2020.2, 2021.8.0, 2021.10.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Threading Building Blocks 2017 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. Homepage: http://software.intel.com/en-us/articles/intel-tbb/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. Homepage: https://github.com/oneapi-src/oneTBB URL: https://github.com/oneapi-src/oneTBB Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ tbl2asn]
| align="center" | [https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ tbl2asn]
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| align="center" | -
| align="center" | -
| align="center" | 6.0.1.5, 8.6.1.6
| align="center" | 6.0.1.5, 8.6.1.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NVIDIA TensorRT is a platform for high-performance deep learning inference Homepage: https://developer.nvidia.com/tensorrt URL: https://developer.nvidia.com/tensorrt Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NVIDIA TensorRT is a platform for high-performance deep learning inference Homepage: https://developer.nvidia.com/tensorrt URL: https://developer.nvidia.com/tensorrt Compatible modules: python/3.10, python/3.11<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/tesseract-ocr/tesseract tesseract]
| align="center" | [https://github.com/tesseract-ocr/tesseract tesseract]
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| align="center" | [https://thrift.apache.org/ thrift]
| align="center" | [https://thrift.apache.org/ thrift]
| align="center" | -
| align="center" | -
| align="center" | 0.13.0, 0.14.2, 0.16.0, 0.18.1
| align="center" | 0.13.0, 0.14.2, 0.16.0, 0.18.1, 0.19.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.10, python/3.11<br /><br /><br /></div>
|-
|-
| align="center" | [http://wiki.tcl.tk/1877 tktable]
| align="center" | [http://wiki.tcl.tk/1877 tktable]
| align="center" | tools
| align="center" | tools
| align="center" | 2.10
| align="center" | 2.10
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl is a simple-to-learn yet very powerful language. Its syntax is described in just a dozen rules, but it has all the features needed to rapidly create useful programs in almost any field of application - on a wide variety of international platforms. Tk is a graphical toolkit for Tcl. It allows you to develop graphical applications that run on Windows, Linux, MacOS X and many other platforms. And not just from Tcl - Tk can be used from many languages including C, Ruby, Perl, Python and Lua. Homepage: http://wiki.tcl.tk/1877 URL: http://wiki.tcl.tk/1877 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl is a simple-to-learn yet very powerful language. Its syntax is described in just a dozen rules, but it has all the features needed to rapidly create useful programs in almost any field of application - on a wide variety of international platforms. Tk is a graphical toolkit for Tcl. It allows you to develop graphical applications that run on Windows, Linux, MacOS X and many other platforms. And not just from Tcl - Tk can be used from many languages including C, Ruby, Perl, Python and Lua. Homepage: http://wiki.tcl.tk/1877 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm]
| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm]
| align="center" | bio
| align="center" | bio
| align="center" | 2.0c
| align="center" | 2.0c
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm URL: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://sourceforge.net/projects/togl/ togl]
| align="center" | [https://sourceforge.net/projects/togl/ togl]
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| align="center" | bio
| align="center" | bio
| align="center" | 2.0.1
| align="center" | 2.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: de novo assembly of RNA-Seq data using ABySS Homepage: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ URL: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: de novo assembly of RNA-Seq data using ABySS Homepage: http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://transdecoder.github.io/ transdecoder]
| align="center" | [https://transdecoder.github.io/ transdecoder]
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| align="center" | 1.0.3
| align="center" | 1.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. Homepage: http://hibberdlab.com/transrate/ URL: http://hibberdlab.com/transrate/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. Homepage: http://hibberdlab.com/transrate/ URL: http://hibberdlab.com/transrate/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.travis-analyzer.de/ travis-analyzer]
| align="center" | -
| align="center" | 220729
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations. Homepage: http://www.travis-analyzer.de/ URL: http://www.travis-analyzer.de/<br /><br /><br /></div>
|-
|-
| align="center" | [http://bitbucket.org/nygcresearch/treemix treemix]
| align="center" | [http://bitbucket.org/nygcresearch/treemix treemix]
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| align="center" | tools
| align="center" | tools
| align="center" | 12.10.1, 12.12.1, 13.0.1, 13.2.0, 13.4.0, 13.4.1
| align="center" | 12.10.1, 12.12.1, 13.0.1, 13.2.0, 13.4.0, 13.4.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. Homepage: https://trilinos.org URL: https://trilinos.org Compatible modules: python/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. Homepage: https://trilinos.org URL: https://trilinos.org Compatible modules: python/3.8, python/3.9, python/3.10 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [http://trimal.cgenomics.org/ trimal]
| align="center" | [http://trimal.cgenomics.org/ trimal]
| align="center" | bio
| align="center" | bio
| align="center" | 1.4
| align="center" | 1.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment Homepage: http://trimal.cgenomics.org/ URL: http://trimal.cgenomics.org/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment Homepage: http://trimal.cgenomics.org/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.usadellab.org/cms/?page=trimmomatic trimmomatic]
| align="center" | [http://www.usadellab.org/cms/?page=trimmomatic trimmomatic]
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| align="center" | bio
| align="center" | bio
| align="center" | 3.0.2, 3.2.0, 3.2.1, 3.2.2, 4.0.0
| align="center" | 3.0.2, 3.2.0, 3.2.1, 3.2.2, 4.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ URL: https://trinotate.github.io/ Extensions: CGI-4.51, Text::NSP-1.31 Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ URL: https://trinotate.github.io/ Extensions: CGI-4.57, Text::NSP-1.31 Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [https://triqs.github.io/triqs triqs]
| align="center" | [https://triqs.github.io/triqs triqs]
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| align="center" | [https://www.openucx.org/ ucc]
| align="center" | [https://www.openucx.org/ ucc]
| align="center" | -
| align="center" | -
| align="center" | 1.0.0
| align="center" | 1.0.0, 1.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. Homepage: https://www.openucx.org/ URL: https://www.openucx.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. Homepage: https://www.openucx.org/ URL: https://www.openucx.org/<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.openucx.org/ ucc-cuda]
| align="center" | [https://www.openucx.org/ ucc-cuda]
| align="center" | -
| align="center" | -
| align="center" | 1.0.0
| align="center" | 1.0.0, 1.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. Homepage: https://www.openucx.org/ URL: https://www.openucx.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. This module adds the UCC CUDA support. Homepage: https://www.openucx.org/ URL: https://www.openucx.org/<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.openucx.org/ ucx]
| align="center" | [https://www.openucx.org/ ucx]
| align="center" | -
| align="center" | -
| align="center" | 1.5.2, 1.6.0, 1.8.0, 1.9.0, 1.10.0, 1.12.1
| align="center" | 1.5.2, 1.6.0, 1.8.0, 1.9.0, 1.10.0, 1.12.1, 1.14.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications Homepage: https://www.openucx.org/ URL: https://www.openucx.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications Homepage: https://www.openucx.org/ URL: https://www.openucx.org/<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.openucx.org/ ucx-cuda]
| align="center" | [http://www.openucx.org/ ucx-cuda]
| align="center" | -
| align="center" | -
| align="center" | 1.12.1
| align="center" | 1.12.1, 1.14.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. Homepage: http://www.openucx.org/ URL: http://www.openucx.org/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. Homepage: http://www.openucx.org/ URL: http://www.openucx.org/<br /><br /><br /></div>
|-
|-
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| align="center" | [https://valgrind.org valgrind-mpi]
| align="center" | [https://valgrind.org valgrind-mpi]
| align="center" | tools
| align="center" | tools
| align="center" | 3.14.0, 3.16.1
| align="center" | 3.14.0, 3.16.1, 3.21.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Valgrind: Debugging and profiling tools Homepage: https://valgrind.org URL: https://valgrind.org Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Valgrind: Debugging and profiling tools Homepage: https://valgrind.org URL: https://valgrind.org Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/dkoboldt/varscan varscan]
| align="center" | [https://github.com/dkoboldt/varscan varscan]
| align="center" | -
| align="center" | -
| align="center" | 2.4.1, 2.4.2
| align="center" | 2.4.1, 2.4.2, 2.4.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Variant calling and somatic mutation/CNV detection for next-generation sequencing data Homepage: https://github.com/dkoboldt/varscan URL: https://github.com/dkoboldt/varscan<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Variant calling and somatic mutation/CNV detection for next-generation sequencing data Homepage: https://github.com/dkoboldt/varscan URL: https://github.com/dkoboldt/varscan<br /><br /><br /></div>
|-
| align="center" | [http://platanus.bio.titech.ac.jp/ vaspkit]
| align="center" | -
| align="center" | 1.5.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLATform for Assembling NUcleotide Sequences Homepage: http://platanus.bio.titech.ac.jp/ URL: http://platanus.bio.titech.ac.jp/<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.vaultproject.io/ vault]
| align="center" | [https://www.vaultproject.io/ vault]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Manage Secrets and Protect Sensitive Data Secure, store and tightly control access to tokens, passwords, certificates, encryption keys for protecting secrets and other sensitive data using a UI, CLI, or HTTP API. Homepage: https://www.vaultproject.io/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Manage Secrets and Protect Sensitive Data Secure, store and tightly control access to tokens, passwords, certificates, encryption keys for protecting secrets and other sensitive data using a UI, CLI, or HTTP API. Homepage: https://www.vaultproject.io/<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/vcflib/vcflib#vcflib vcflib]
| align="center" | [https://github.com/vcflib/vcflib vcflib]
| align="center" | -
| align="center" | -
| align="center" | 1.0.1, 1.0.3
| align="center" | 1.0.1, 1.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed variations between individuals. VCF provides a common interchange format for the description of variation in individuals and populations of samples, and has become the defacto standard reporting format for a wide array of genomic variant detectors. vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both: - an API for parsing and operating on records of genomic variation as it can be described by the VCF format, - and a collection of command-line utilities for executing complex manipulations on VCF files. The API itself provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. Homepage: https://github.com/vcflib/vcflib#vcflib URL: https://github.com/vcflib/vcflib#vcflib<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals. Homepage: https://github.com/vcflib/vcflib URL: https://github.com/vcflib/vcflib<br /><br /><br /></div>
|-
|-
| align="center" | [https://vcftools.github.io vcftools]
| align="center" | [https://vcftools.github.io vcftools]
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| align="center" | bio
| align="center" | bio
| align="center" | 1.2.10
| align="center" | 1.2.10
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sequence assembler for very short reads Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ URL: http://www.ebi.ac.uk/~zerbino/velvet/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sequence assembler for very short reads Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://csg.sph.umich.edu/kang/verifyBamID/index.html verifybamid]
| align="center" | [http://csg.sph.umich.edu/kang/verifyBamID/index.html verifybamid]
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| align="center" | [https://www.ks.uiuc.edu/Research/vmd vmd]
| align="center" | [https://www.ks.uiuc.edu/Research/vmd vmd]
| align="center" | vis
| align="center" | vis
| align="center" | 1.9.3, 1.9.4a43
| align="center" | 1.9.3, 1.9.4a43, 1.9.4a57
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Homepage: https://www.ks.uiuc.edu/Research/vmd URL: https://www.ks.uiuc.edu/Research/vmd Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Homepage: https://www.ks.uiuc.edu/Research/vmd URL: https://www.ks.uiuc.edu/Research/vmd Keyword:vis<br /><br /><br /></div>
|-
|-
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| align="center" | math
| align="center" | math
| align="center" | 0.4.6
| align="center" | 0.4.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Homepage: http://math.lbl.gov/voro++/ URL: http://math.lbl.gov/voro++/ Keyword:math<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Homepage: http://math.lbl.gov/voro++/ Keyword:math<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/torognes/vsearch vsearch]
| align="center" | [https://github.com/torognes/vsearch vsearch]
| align="center" | bio
| align="center" | bio
| align="center" | 2.5.0, 2.9.1, 2.13.3, 2.13.4, 2.15.2, 2.21.1
| align="center" | 2.5.0, 2.9.1, 2.13.3, 2.13.4, 2.15.2, 2.21.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. VSEARCH uses an optimal global aligner (full dynamic programming Needleman-Wunsch), in contrast to USEARCH which by default uses a heuristic seed and extend aligner. This usually results in more accurate alignments and overall improved sensitivity (recall) with VSEARCH, especially for alignments with gaps. Homepage: https://github.com/torognes/vsearch Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. Homepage: https://github.com/torognes/vsearch URL: https://github.com/torognes/vsearch Keyword:bio<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.vtk.org vtk]
| align="center" | [http://www.vtk.org vtk]
| align="center" | vis
| align="center" | vis
| align="center" | 6.3.0, 8.0.0, 8.1.1, 8.2.0, 9.0.1, 9.1.0
| align="center" | 6.3.0, 8.0.0, 8.1.1, 8.2.0, 9.0.1, 9.1.0, 9.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org URL: http://www.vtk.org Compatible modules: python/3.5.4, python/3.6.3, python/3.7.4 Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org URL: http://www.vtk.org Compatible modules: python/3.11, python/3.10 Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.vtk.org vtk-mpi]
| align="center" | [http://www.vtk.org vtk-mpi]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org URL: http://www.vtk.org Compatible modules: python/3.8, python/3.7, python/3.6 Keyword:vis<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org URL: http://www.vtk.org Compatible modules: python/3.8, python/3.7, python/3.6 Keyword:vis<br /><br /><br /></div>
|-
|-
| align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/vtune-profiler.html vtune]
| align="center" | [https://software.intel.com/en-us/vtune vtune]
| align="center" | tools
| align="center" | tools
| align="center" | 2018.3, 2019.3, 2020.1, 2022.2
| align="center" | 2018.3, 2019.3, 2020.1, 2022.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel VTune Profiler is a performance analysis tool for C, C++, C#, Fortran, Java, Python, Go, DPC++, and OpenCL. Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/vtune-profiler.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/vtune-profiler.html Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Homepage: https://software.intel.com/en-us/vtune URL: https://software.intel.com/en-us/vtune Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/NOAA-EMC/NCEPLIBS-w3emc/ w3emc]
| align="center" | -
| align="center" | 2.11.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This library contains Fortran decoder/encoder routines for GRIB edition 1. GRIdded Binary or General Regularly-distributed Information in Binary form (GRIB) is a World Meteorological Organization (WMO) standard for gridded data. This is part of the NCEPLIBS project. Homepage: hthttps://github.com/NOAA-EMC/NCEPLIBS-w3emc/ URL: hthttps://github.com/NOAA-EMC/NCEPLIBS-w3emc/<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.wannier.org/ wannier90]
| align="center" | [http://www.wannier.org/ wannier90]
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| align="center" | [https://code.ornl.gov/neams-workbench/wasp wasp]
| align="center" | [https://code.ornl.gov/neams-workbench/wasp wasp]
| align="center" | -
| align="center" | -
| align="center" | 3.1.4, 4.0.3
| align="center" | 3.1.4, 4.0.3, 4.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files. Homepage: https://code.ornl.gov/neams-workbench/wasp URL: https://code.ornl.gov/neams-workbench/wasp<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Workbench Analysis Sequence Processor (WASP) was developed to streamline lexing, parsing, access, validation, and analysis of ascii text files. Homepage: https://code.ornl.gov/neams-workbench/wasp URL: https://code.ornl.gov/neams-workbench/wasp<br /><br /><br /></div>
|-
|-
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| align="center" | geo
| align="center" | geo
| align="center" | 3.9.1, 4.1, 4.2
| align="center" | 3.9.1, 4.1, 4.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Compiled with -DNO_LEAP_CALENDAR. The WPS Geographical Input Data are included in the geog directory. Homepage: http://www.wrf-model.org Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Homepage: http://www.wrf-model.org URL: http://www.wrf-model.org Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.wrf-model.org wrf]
| align="center" | [https://www.wrf-model.org wrf]
| align="center" | geo
| align="center" | geo
| align="center" | 3.9.1.1, 4.1.3, 4.2.1, 4.3.3
| align="center" | 3.9.1.1, 4.1.3, 4.2.1, 4.3.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Compiled with -DNO_LEAP_CALENDAR Homepage: http://www.wrf-model.org Keyword:geo<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. Homepage: https://www.wrf-model.org URL: https://www.wrf-model.org Keyword:geo<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/ruanjue/wtdbg2 wtdbg2]
| align="center" | [https://github.com/ruanjue/wtdbg2 wtdbg2]
| align="center" | -
| align="center" | -
| align="center" | 2.5
| align="center" | 2.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy. Homepage: https://github.com/ruanjue/wtdbg2 URL: https://github.com/ruanjue/wtdbg2<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output Homepage: https://github.com/ruanjue/wtdbg2 URL: https://github.com/ruanjue/wtdbg2<br /><br /><br /></div>
|-
|-
| align="center" | [https://www.wxwidgets.org wxwidgets]
| align="center" | [https://www.wxwidgets.org wxwidgets]
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| align="center" | 3.1.1, 3.1.4, 3.1.7
| align="center" | 3.1.1, 3.1.4, 3.1.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. Homepage: https://www.wxwidgets.org URL: https://www.wxwidgets.org Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: wxPython-4.1.1 Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. Homepage: https://www.wxwidgets.org URL: https://www.wxwidgets.org Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: wxPython-4.1.1 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/XBraid/xbraid xbraid]
| align="center" | -
| align="center" | 3.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: XBraid is a parallel-in-time software package. It implements an optimal-scaling multigrid solver for the (non)linear systems that arise from the discretization of problems with evolutionary behavior. Homepage: https://github.com/XBraid/xbraid URL: https://github.com/XBraid/xbraid<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.xcrysden.org/ xcrysden]
| align="center" | [http://www.xcrysden.org/ xcrysden]
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| align="center" | [https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod xml-libxml]
| align="center" | [https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod xml-libxml]
| align="center" | -
| align="center" | -
| align="center" | 2.0205
| align="center" | 2.0205, 2.0208
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Perl binding for libxml2 Homepage: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod URL: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod Extensions: Alien::Base-2.23, Alien::Libxml2-0.16, File::chdir-0.1010, XML::LibXML-2.0205<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Perl binding for libxml2 Homepage: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod URL: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod Extensions: Alien::Base-2.80, Alien::Build::Plugin::Download::GitLab-0.01, Alien::Libxml2-0.19, File::chdir-0.1011, XML::LibXML-2.0208<br /><br /><br /></div>
|-
|-
| align="center" | [https://launchpad.net/xmlf90/ xmlf90]
| align="center" | [https://gitlab.com/siesta-project/libraries/xmlf90 xmlf90]
| align="center" | tools
| align="center" | tools
| align="center" | 1.5.4
| align="center" | 1.5.4, 1.6.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xmlf90 is a suite of libraries to handle XML in Fortran. It has two major components: - A XML parsing library. The parser was designed to be a useful tool in the extraction and analysis of data in the context of scientific computing, and thus the priorities were efficiency and the ability to deal with very large XML files while maintaining a small memory footprint. The most complete programming interface is based on the very successful SAX (Simple API for XML) model, although a partial DOM interface and a very experimental XPATH interface are also present. - A library (xmlf90-wxml) that facilitates the writing of well-formed XML, including such features as automatic start-tag completion, attribute pretty-printing, and element indentation. There are also helper routines to handle the output of numerical arrays. Homepage: https://launchpad.net/xmlf90/ URL: https://launchpad.net/xmlf90/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A fast XML parser and generator in Fortran Homepage: https://gitlab.com/siesta-project/libraries/xmlf90 URL: https://gitlab.com/siesta-project/libraries/xmlf90 Keyword:tools<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/grimme-lab/xtb xtb]
| align="center" | [https://github.com/grimme-lab/xtb xtb]
| align="center" | chem
| align="center" | chem
| align="center" | 6.3.0, 6.3.3, 6.4.0, 6.4.1, 6.5.0, 6.5.1
| align="center" | 6.3.0, 6.3.3, 6.4.0, 6.4.1, 6.5.0, 6.5.1, 6.6.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtb - Extended tight-binding semi-empirical quantum mechanics Homepage: https://github.com/grimme-lab/xtb URL: https://github.com/grimme-lab/xtb Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: ase-3.22.1, Pint-0.19.2, pydantic-1.9.1, qcelemental-0.24.0, xtb-6.5.0 Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtb - Extended tight-binding semi-empirical quantum mechanics Homepage: https://github.com/grimme-lab/xtb URL: https://github.com/grimme-lab/xtb Compatible modules: python/3.10, python/3.11 Extensions: ase-3.22.1, Pint-0.22, pydantic-1.9.1, qcelemental-0.27.1, xtb-6.6.1 Keyword:chem<br /><br /><br /></div>
|-
|-
| align="center" | [https://github.com/xtensor-stack/xtensor xtensor]
| align="center" | [https://github.com/xtensor-stack/xtensor xtensor]
Line 5,347: Line 5,477:
| align="center" | [https://www.dkrz.de/redmine/projects/yaxt yaxt]
| align="center" | [https://www.dkrz.de/redmine/projects/yaxt yaxt]
| align="center" | tools
| align="center" | tools
| align="center" | 0.5.1, 0.6.0, 0.9.0, 0.9.1
| align="center" | 0.5.1, 0.6.0, 0.9.0, 0.9.1, 0.10.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt URL: https://www.dkrz.de/redmine/projects/yaxt Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt URL: https://www.dkrz.de/redmine/projects/yaxt Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.zeoplusplus.org/ zeo++]
| align="center" | -
| align="center" | 0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Zeo++ is a software package for analysis of crystalline porous materials. Zeo++ can be used to perform geometry-based analysis of structure and topology of the void space inside a material, to assemble or alternate structures as well as to generate structure representations to be used in structure similarity calculations. Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database. Homepage: https://www.zeoplusplus.org/ URL: https://www.zeoplusplus.org/<br /><br /><br /></div>
|-
|-
| align="center" | [http://www.zeromq.org/ zeromq]
| align="center" | [http://www.zeromq.org/ zeromq]
Oldeman
cc_staff
153

edits

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