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<noinclude>{{NOINDEX}}</noinclude>
! style="width: 25%" align="center" | Module
! style="width: 15%" align="center" | Type
! style="width: 30%" align="center" | Versions
! align="center" | Description
|-
| align="center" | [http://www.simulia.com/products/abaqus_fea.html abaqus]
| align="center" | phys
| align="center" | 6.14.1, 2020, 2021
| Documentation: [[Abaqus]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. Homepage: http://www.simulia.com/products/abaqus_fea.html URL: http://www.simulia.com/products/abaqus_fea.html Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://www.abinit.org/ abinit]
| align="center" | chem
| align="center" | 8.2.2, 8.4.4, 8.8.4, 8.10.2
| Documentation: [[ABINIT]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. Homepage: http://www.abinit.org/ URL: http://www.abinit.org/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.bcgsc.ca/platform/bioinfo/software/abyss abyss]
| align="center" | bio
| align="center" | 1.5.2, 1.9.0
| <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: http://www.bcgsc.ca/platform/bioinfo/software/abyss Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://sourceforge.net/projects/actc actc]
| align="center" | -
| align="center" | 1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc<br /><br /><br /></div>
|-
| align="center" | [http://software.genetics.ucla.edu/admixture admixture]
| align="center" | bio
| align="center" | 1.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: http://software.genetics.ucla.edu/admixture URL: http://software.genetics.ucla.edu/admixture Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://software.intel.com/intel-advisor-xe advisor]
| align="center" | tools
| align="center" | 2018.3, 2019.3, 2020.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Vectorization Optimization and Thread Prototyping - Vectorize and thread code or performance dies - Easy workflow + data + tips = faster code faster - Prioritize, Prototype and Predict performance gain Homepage: https://software.intel.com/intel-advisor-xe URL: https://software.intel.com/intel-advisor-xe Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://afni.nimh.nih.gov/ afni]
| align="center" | bio
| align="center" | 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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/horta/almosthere almosthere]
| align="center" | -
| align="center" | 1.0.10
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program. Homepage: https://github.com/horta/almosthere URL: https://github.com/horta/almosthere<br /><br /><br /></div>
|-
| align="center" | [https://github.com/ALPSCore/ALPSCore alpscore]
| align="center" | phys
| align="center" | 2.2.0
| <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 Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://www.popgen.dk/angsd angsd]
| align="center" | bio
| align="center" | 0.918
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://annovar.openbioinformatics.org/en/latest/ annovar]
| align="center" | bio
| align="center" | 2017Jul16, 20191024
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Homepage: http://annovar.openbioinformatics.org/en/latest/ URL: http://annovar.openbioinformatics.org/en/latest/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/castorini/anserini anserini]
| align="center" | -
| align="center" | 0.9.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open-source information retreival toolkit built on Lucene that aims to bridge the gap between academic information retrieval and the practice of building real-world search applications. Usage: Binaries located in Anserini's target/appassembler/bin are on path. Anserini's folders bin, collections, docs, indexes, logs, runs, src, target, tools, as well as the files pom.xml and README.md are available at $EBROOTANSERINI. Eg. Indexing command for help: IndexCollection -h Homepage: https://github.com/castorini/anserini URL: https://github.com/castorini/anserini<br /><br /><br /></div>
|-
| align="center" | [http://www.ansys.com ansys]
| align="center" | phys
| align="center" | 16.2.3, 17.2, 18.1, 18.2, 19.1, 19.2, 2019R2, 2019R3, 2020R1, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2
| Documentation: [[Ansys]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://www.ansys.com ansysedt]
| align="center" | -
| align="center" | 2021R2, 2023R2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com<br /><br /><br /></div>
|-
| align="center" | [https://ant.apache.org/ ant]
| align="center" | tools
| align="center" | 1.9.15, 1.10.8
| <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>
|-
| align="center" | [https://github.com/appleseedhq/appleseed appleseed]
| align="center" | vis
| align="center" | 1.8.1-beta
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: appleseed is an open source, physically-based global illumination rendering engine primarily designed for animation and visual effects. Homepage: https://github.com/appleseedhq/appleseed Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://apptainer.org apptainer]
| align="center" | -
| align="center" | 1.1.3, 1.1.5, 1.1.6, 1.1.8, 1.2.4
| <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>
|-
| align="center" | [http://arma.sourceforge.net/ armadillo]
| align="center" | math
| align="center" | 7.950.1, 8.500.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Homepage: http://arma.sourceforge.net/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://forge.scilab.org/index.php/p/arpack-ng/ arpack-ng]
| align="center" | math
| align="center" | 3.4.0, 3.5.0
| <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: http://forge.scilab.org/index.php/p/arpack-ng/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://downloads.asperasoft.com/ ascp]
| align="center" | tools
| 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/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://bioinf.uni-greifswald.de/augustus/ augustus]
| align="center" | bio
| align="center" | 3.3.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Homepage: http://bioinf.uni-greifswald.de/augustus/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://vina.scripps.edu/index.html autodock_vina]
| align="center" | chem
| 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>
|-
| align="center" | [https://github.com/pezmaster31/bamtools bamtools]
| align="center" | bio
| align="center" | 2.4.1
| <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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://genome.sph.umich.edu/wiki/BamUtil bamutil]
| align="center" | bio
| align="center" | 1.0.13
| <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" | [http://bazel.io/ bazel]
| align="center" | tools
| align="center" | 0.5.2, 0.7.0, 0.11.1, 0.19.2, 0.25.2, 0.27.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Homepage: http://bazel.io/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://sourceforge.net/projects/bbmap/ bbmap]
| align="center" | bio
| align="center" | 37.36, 38.86
| <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" | [http://www.htslib.org/ bcftools]
| align="center" | bio
| align="center" | 1.4, 1.5, 1.9
| <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: http://www.htslib.org/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://faculty.washington.edu/browning/beagle/beagle.html beagle]
| align="center" | -
| align="center" | 5.4
| <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>
|-
| align="center" | [https://github.com/beagle-dev/beagle-lib beagle-lib]
| align="center" | bio
| align="center" | 2.1.2
| <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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://beast2.org/ beast]
| align="center" | bio
| align="center" | 1.8.2, 2.4.0
| <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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://bedops.readthedocs.io/en/latest/index.html bedops]
| align="center" | -
| align="center" | 2.4.35
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. Homepage: http://bedops.readthedocs.io/en/latest/index.html<br /><br /><br /></div>
|-
| align="center" | [https://github.com/arq5x/bedtools2 bedtools]
| align="center" | bio
| align="center" | 2.26.0, 2.27.1, 2.29.0
| <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>
|-
| align="center" | [http://dx.doi.org/10.1103/PhysRevB.85.235149. beef]
| align="center" | chem
| align="center" | 0.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. Homepage: http://suncat.stanford.edu/facility/software/functional URL: http://suncat.stanford.edu/facility/software/functional Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://arxiv.org/abs/1111.4429). berkeleygw]
| align="center" | phys
| align="center" | 1.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. We ask that you please cite the following papers when using results obtained from the BerkeleyGW package: - Mark S. Hybertsen and Steven G. Louie, Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies, Phys. Rev. B 34, 5390 (1986). - Michael Rohlfing and Steven G. Louie, Electron-hole excitations and optical spectra from first principles, Phys. Rev. B 62, 4927 (2000). - Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, and Steven G. Louie, BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures, Comput. Phys. Commun. 183, 1269 (2012) (https://arxiv.org/abs/1111.4429). Homepage: http://www.berkeleygw.org Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [https://bioperl.org/ bioperl]
| align="center" | bio
| 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: 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://www.gnu.org/software/bison bison]
| align="center" | -
| align="center" | 3.7.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. Homepage: https://www.gnu.org/software/bison URL: https://www.gnu.org/software/bison<br /><br /><br /></div>
|-
| align="center" | [https://github.com/PacificBiosciences/blasr blasr]
| align="center" | bio
| align="center" | 5.3.0
| <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>
|-
| align="center" | [http://blast.ncbi.nlm.nih.gov/ blast]
| align="center" | bio
| align="center" | 2.2.26
| <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: http://blast.ncbi.nlm.nih.gov/ URL: http://blast.ncbi.nlm.nih.gov/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://blast.ncbi.nlm.nih.gov/ blast+]
| align="center" | bio
| align="center" | 2.6.0, 2.9.0
| 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: http://blast.ncbi.nlm.nih.gov/ URL: http://blast.ncbi.nlm.nih.gov/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://genome.ucsc.edu/FAQ/FAQblat.html blat]
| align="center" | bio
| align="center" | 3.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. - Homepage: http://genome.ucsc.edu/FAQ/FAQblat.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.blender.org/ blender]
| align="center" | vis
| align="center" | 3.6.0
| <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" | -
| align="center" | 0.8.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. Homepage: https://github.com/flame/blis/ URL: https://github.com/flame/blis/<br /><br /><br /></div>
|-
| align="center" | [https://www.blosc.org/ blosc]
| align="center" | -
| align="center" | 1.17.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Blosc, an extremely fast, multi-threaded, meta-compressor library Homepage: https://www.blosc.org/ URL: https://www.blosc.org/<br /><br /><br /></div>
|-
| align="center" | [https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ bolt-lmm]
| align="center" | bio
| align="center" | 2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations). The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM). The BOLT-REML algorithm estimates heritability explained by genotyped SNPs and genetic correlations among multiple traits measured on the same set of individuals. Like the GCTA software. Homepage: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.boost.org/ boost]
| align="center" | tools
| align="center" | 1.60.0, 1.63.0, 1.65.1, 1.68.0, 1.72.0
| <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/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.boost.org/ boost-mpi]
| align="center" | tools
| align="center" | 1.60.0, 1.65.1, 1.68.0, 1.72.0
| <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/2.7, python/3.6, python/3.7, python/3.8 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://bowtie-bio.sourceforge.net/index.shtml bowtie]
| align="center" | bio
| align="center" | 1.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. - Homepage: http://bowtie-bio.sourceforge.net/index.shtml Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2]
| align="center" | bio
| align="center" | 2.3.0, 2.3.3.1, 2.3.5
| <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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/BUStools/bustools bustools]
| align="center" | -
| align="center" | 0.40.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow. Homepage: https://github.com/BUStools/bustools URL: https://github.com/BUStools/bustools<br /><br /><br /></div>
|-
| align="center" | [http://bio-bwa.sourceforge.net/ bwa]
| align="center" | bio
| 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>
|-
| align="center" | [https://github.com/caffe2/caffe2 caffe2]
| align="center" | ai
| align="center" | 0.8.1
| Documentation: [[Caffe2]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Caffe2 is a lightweight, modular, and scalable deep learning framework. Building on the original Caffe, Caffe2 is designed with expression, speed, and modularity in mind. Homepage: https://github.com/caffe2/caffe2 Keyword:ai<br /><br /><br /></div>
|-
| align="center" | [https://github.com/marbl/canu canu]
| align="center" | bio
| align="center" | 1.5, 1.6, 1.7.1, 1.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences Homepage: https://github.com/marbl/canu Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/Illumina/canvas canvas]
| align="center" | bio
| align="center" | 1.25
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome. To run, do mono $EBROOTCANVAS/Canvas.dll ... Homepage: https://github.com/Illumina/canvas Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://seq.cs.iastate.edu/ cap3]
| align="center" | bio
| 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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/catchorg/Catch2 catch2]
| align="center" | -
| align="center" | 2.11.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch) Homepage: https://github.com/catchorg/Catch2 URL: https://github.com/catchorg/Catch2<br /><br /><br /></div>
|-
| align="center" | [http://www.cesm.ucar.edu/models/ccsm4.0/ ccsm]
| align="center" | geo
| 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/ Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [https://code.zmaw.de/projects/cdo cdo]
| align="center" | geo
| align="center" | 1.7.2
| <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 Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome cellranger]
| align="center" | bio
| 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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/infphilo/centrifuge centrifuge]
| align="center" | bio
| align="center" | 1.0.3-beta
| <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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://uscilab.github.io/cereal/ cereal]
| align="center" | -
| align="center" | 1.3.0
| <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>
|-
| align="center" | [http://www.cesm.ucar.edu/models/cesm2/ cesm]
| align="center" | geo
| 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/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" | vis
| align="center" | 3.42, 3.48
| <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>
|-
| align="center" | [https://www.cgal.org/ cgal]
| align="center" | math
| align="center" | 4.9, 4.14.3, 5.5.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. Homepage: https://www.cgal.org/ URL: https://www.cgal.org/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://cgns.github.io/ cgns]
| align="center" | phys
| align="center" | 3.3.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data. Homepage: https://cgns.github.io/ Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://chapel.cray.com chapel-single]
| align="center" | tools
| align="center" | 1.15.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI. Homepage: http://chapel.cray.com Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://chapel.cray.com chapel-slurm-gasnetrun_ibv]
| align="center" | tools
| align="center" | 1.15.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Chapel is an emerging parallel programming language whose design and development is being led by Cray Inc. Chapel is designed to improve the productivity of high-end computer users while also serving as a portable parallel programming model that can be used on commodity clusters or desktop multicore systems. Chapel strives to vastly improve the programmability of large-scale parallel computers while matching or beating the performance and portability of current programming models like MPI. Homepage: http://chapel.cray.com Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://circos.ca/documentation/ circos]
| align="center" | vis
| align="center" | 0.69-6
| <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>
|-
| align="center" | [http://clang.llvm.org/ clang]
| align="center" | tools
| align="center" | 3.8.1, 3.9.0
| <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: http://clang.llvm.org/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://proj-clhep.web.cern.ch/proj-clhep/ clhep]
| align="center" | math
| align="center" | 2.3.1.1, 2.4.1.0, 2.4.1.2
| <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: http://proj-clhep.web.cern.ch/proj-clhep/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://www.cmake.org cmake]
| align="center" | tools
| align="center" | 3.12.3, 3.16.3, 3.18.4, 3.20.1, 3.21.4, 3.22.1, 3.23.1, 3.27.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. Homepage: https://www.cmake.org URL: https://www.cmake.org Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/abyzovlab/CNVnator cnvnator]
| align="center" | bio
| align="center" | 0.3.3
| <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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/cdr/code-server code-server]
| align="center" | -
| align="center" | 3.4.1, 3.5.0, 3.12.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Run VS Code on any machine anywhere and access it in the browser. Homepage: https://github.com/cdr/code-server URL: https://github.com/cdr/code-server<br /><br /><br /></div>
|-
| align="center" | [https://projects.coin-or.org/CoinMP coinmp]
| align="center" | -
| align="center" | 1.8.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CoinMP is a C-API library that supports most of the functionality of CLP (Coin LP), CBC (Coin Branch-and-Cut), and CGL (Cut Generation Library) projects. Homepage: https://projects.coin-or.org/CoinMP URL: https://projects.coin-or.org/CoinMP<br /><br /><br /></div>
|-
| align="center" | [https://www.comsol.com comsol]
| align="center" | phys
| align="center" | 5.3a, 5.4, 5.5, 5.6, 6.0.0.405, 6.1, 6.1.0.357, 6.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com URL: https://www.comsol.com Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [https://github.com/Oshlack/Corset/wiki corset]
| align="center" | bio
| align="center" | 1.09
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts. Our software takes a set of reads that have been multi-mapped to the transcriptome (where multiple alignments per read were reported) and hierarchically clusters the transcripts based on the proportion of shared reads and expression patterns. It will report the clusters and gene-level counts for each sample, which are easily tested for differential expression with count based tools such as edgeR and DESeq. Homepage: https://github.com/Oshlack/Corset/wiki URL: https://github.com/Oshlack/Corset/wiki Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.cp2k.org/ cp2k]
| align="center" | chem
| align="center" | 4.1, 6.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. Homepage: http://www.cp2k.org/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://cpmd.org cpmd]
| align="center" | chem
| align="center" | 3.17.1
| Documentation: [[CPMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. Homepage: http://cpmd.org Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://github.com/zeromq/cppzmq cppzmq]
| align="center" | -
| align="center" | 4.7.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cppzmq is a C++ binding for libzmq Homepage: https://github.com/zeromq/cppzmq URL: https://github.com/zeromq/cppzmq<br /><br /><br /></div>
|-
| align="center" | [http://cromwell.readthedocs.io/ cromwell]
| align="center" | tools
| align="center" | 34, 58
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scientific workflow engine designed for simplicity and scalability. Trivially transition between one off use cases to massive scale production environments http://cromwell.readthedocs.io/ Homepage: https://cromwell.readthedocs.io/ URL: https://cromwell.readthedocs.io/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.cst.com/ cst]
| align="center" | phys
| align="center" | 2018, 2020
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CST offers accurate, efficient computational solutions for electromagnetic design and analysis. CST simulation is user-friendly and enables users to choose the most appropriate method for the design and optimization of devices operating in a wide range of frequencies. Please note that we installed only Graphic frontend and command line interface. You need to provide your own license server in order to be able to run CST. Homepage: https://www.cst.com/ URL: https://www.cst.com/ Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [https://github.com/shenwei356/csvtk csvtk]
| align="center" | -
| align="center" | 0.23.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Similar to FASTA/Q format in field of Bioinformatics, CSV/TSV formats are basic and ubiquitous file formats in both Bioinformatics and data science. People usually use spreadsheet software like MS Excel to process table data. However this is all by clicking and typing, which is not automated and is time-consuming to repeat, especially when you want to apply similar operations with different datasets or purposes. You can also accomplish some CSV/TSV manipulations using shell commands, but more code is needed to handle the header line. Shell commands do not support selecting columns with column names either. csvtk is convenient for rapid data investigation and also easy to integrate into analysis pipelines. It could save you lots of time in (not) writing Python/R scripts. Homepage: https://github.com/shenwei356/csvtk URL: https://github.com/shenwei356/csvtk<br /><br /><br /></div>
|-
| align="center" | [https://feynarts.de/cuba/ cuba]
| align="center" | -
| align="center" | 4.2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Cuba a library for multidimensional numerical integration Homepage: https://feynarts.de/cuba/ URL: https://feynarts.de/cuba/<br /><br /><br /></div>
|-
| align="center" | [https://developer.nvidia.com/cuda-toolkit cuda]
| align="center" | tools
| align="center" | 7.5.18, 8.0.44, 10.1, 11.0, 11.1.1, 11.2.2
| Documentation: [[CUDA]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. Homepage: https://developer.nvidia.com/cuda-toolkit URL: https://developer.nvidia.com/cuda-toolkit Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://developer.nvidia.com/cudnn cudnn]
| align="center" | math
| align="center" | 5.1, 6.0, 7.0, 7.6.5, 8.0.3, 8.2.0, 8.6.0.163, 8.7.0.84, 8.9.5.29
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. Homepage: https://developer.nvidia.com/cudnn URL: https://developer.nvidia.com/cudnn Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://cole-trapnell-lab.github.io/cufflinks/ cufflinks]
| align="center" | bio
| align="center" | 2.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq - Homepage: http://cole-trapnell-lab.github.io/cufflinks/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://sourceforge.net/projects/cunit/ cunit]
| align="center" | tools
| align="center" | 2.1-3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Automated testing framework for C. Homepage: https://sourceforge.net/projects/cunit/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://docs.nvidia.com/cuda/cusparselt/index.html cusparselt]
| align="center" | -
| align="center" | 0.4.0.7
| <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" | -
| align="center" | 1.1
| <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" | -
| align="center" | 1.5.0.3, 1.7.0.1
| <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>
|-
| align="center" | [https://sourceforge.net/projects/cvit/ cvit]
| align="center" | -
| align="center" | 1.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A genomic linkage feature visualization tools based on Perl. Homepage: https://sourceforge.net/projects/cvit/ URL: https://sourceforge.net/projects/cvit/ Extensions: Config::IniFiles-3.000002, Data::Dumper-2.173, ExtUtils::PkgConfig-1.16, GD-2.71, GD::Arrow-0.01, GD::SVG-0.33, GD::Text-0.86, SVG-2.84, Test::Fork-0.02<br /><br /><br /></div>
|-
| align="center" | [https://dakota.sandia.gov/ dakota]
| align="center" | tools
| align="center" | 6.8, 6.13
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. The Dakota toolkit provides a flexible, extensible interface between such simulation codes and its iterative systems analysis methods, which include: - optimization with gradient and nongradient-based methods; - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods; - parameter estimation using nonlinear least squares (deterministic) or Bayesian inference (stochastic); and - sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization, surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. Homepage: https://dakota.sandia.gov/ URL: https://dakota.sandia.gov/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/rordenlab/dcm2niix dcm2niix]
| align="center" | bio
| align="center" | 1.0.20200331
| <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>
|-
| align="center" | [http://www.allinea.com ddt-cpu]
| align="center" | tools
| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1
| 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>
|-
| align="center" | [http://www.allinea.com ddt-gpu]
| align="center" | tools
| align="center" | 7.1, 18.3, 19.1.4, 20.2, 22.0.1
| 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>
|-
| align="center" | [http://www.dealii.org/ dealii]
| align="center" | math
| align="center" | 8.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A C++ software library supporting the creation of finite element codes and an open community of users and developers. Homepage: http://www.dealii.org/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://github.com/dellytools/delly delly]
| align="center" | -
| align="center" | 0.7.8, 0.8.5
| <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. Homepage: https://github.com/dellytools/delly URL: https://github.com/dellytools/delly<br /><br /><br /></div>
|-
| align="center" | [https://github.com/bbuchfink/diamond diamond]
| align="center" | bio
| align="center" | 0.9.8, 0.9.22, 0.9.32
| <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>
|-
| align="center" | [http://www.scd.stfc.ac.uk/SCD/44516.aspx dl_poly4]
| align="center" | chem
| align="center" | 4.08
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. Homepage: http://www.scd.stfc.ac.uk/SCD/44516.aspx Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://github.com/nanoporetech/dorado dorado]
| align="center" | -
| align="center" | 0.2.1, 0.2.2, 0.3.0
| <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>
|-
| align="center" | [https://www.microsoft.com/net/ dotnet-core]
| align="center" | -
| align="center" | 3.0.0, 3.1.8, 5.0.12, 6.0.0
| <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. Contains the SDK and the Runtime. Homepage: https://www.microsoft.com/net/ URL: https://www.microsoft.com/net/<br /><br /><br /></div>
|-
| align="center" | [https://www.microsoft.com/net/ dotnet-core-runtime]
| align="center" | tools
| 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. Homepage: https://www.microsoft.com/net/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/google/double-conversion double-conversion]
| align="center" | -
| align="center" | 3.1.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. Homepage: https://github.com/google/double-conversion URL: https://github.com/google/double-conversion<br /><br /><br /></div>
|-
| align="center" | [https://www.perl.org/ eclipse]
| align="center" | tools
| 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>
|-
| align="center" | [https://eigen.tuxfamily.org/index.php?title=Main_Page eigen]
| align="center" | math
| align="center" | 3.2.2, 3.2.10, 3.3.2, 3.3.5, 3.3.7
| <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>
|-
| align="center" | [https://elpa.rzg.mpg.de elpa]
| align="center" | math
| align="center" | 2017.11.001, 2020.05.001
| <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>
|-
| align="center" | [http://emboss.sourceforge.net/ emboss]
| align="center" | bio
| align="center" | 6.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. Homepage: http://emboss.sourceforge.net/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/embree/embree embree]
| align="center" | -
| align="center" | 3.11.0
| <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>
|-
| align="center" | [https://energyplus.net/downloads energyplus]
| align="center" | -
| align="center" | 9.3.0, 23.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumptionfor heating, cooling, ventilation, lighting and plug and process loadsand water use in buildings. Homepage: https://energyplus.net/downloads URL: https://energyplus.net/downloads<br /><br /><br /></div>
|-
| align="center" | [https://github.com/grimme-lab/enso enso]
| align="center" | -
| align="center" | 1.271
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Energetic sorting of conformer rotamer ensembles Homepage: https://github.com/grimme-lab/enso URL: https://github.com/grimme-lab/enso<br /><br /><br /></div>
|-
| align="center" | [http://www.erlang.org/ erlangotp]
| align="center" | tools
| align="center" | 20.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Erlang is a general-purpose concurrent, garbage-collected programming language and runtime system. Homepage: http://www.erlang.org/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://sourceforge.net/projects/esmf esmf]
| align="center" | geo
| align="center" | 7.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. Homepage: http://sourceforge.net/projects/esmf Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [http://www.etsf.eu/resources/software/libraries_and_tools etsf_io]
| align="center" | io
| align="center" | 1.0.4
| <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 Keyword:io<br /><br /><br /></div>
|-
| align="center" | [http://www.etsf.eu/resources/software/libraries_and_tools etsf_io-mpi]
| align="center" | -
| align="center" | 1.0.4
| <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>
|-
| align="center" | [http://www.ebi.ac.uk/~guy/exonerate/ exonerate]
| align="center" | bio
| 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: http://www.ebi.ac.uk/~guy/exonerate/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://libexpat.github.io expat]
| align="center" | tools
| align="center" | 2.2.5, 2.2.6, 2.2.9, 2.2.10
| <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://bitbucket.org/jerlar73/fast-gbs fast-gbs]
| align="center" | bio
| align="center" | 2017-01-25
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A bioinformatic pipeline designed to extract a high-quality SNP catalog starting from FASTQ files obtained from sequencing genotyping-by-sequencing (GBS) libraries. Homepage: https://bitbucket.org/jerlar73/fast-gbs Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.atgc-montpellier.fr/fastme/ fastme]
| align="center" | bio
| align="center" | 2.1.6.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. Homepage: http://www.atgc-montpellier.fr/fastme/ URL: http://www.atgc-montpellier.fr/fastme/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc]
| align="center" | bio
| align="center" | 0.11.5, 0.11.8, 0.11.9, 0.12.0
| <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>
|-
| align="center" | [http://fastqtl.sourceforge.net/ fastqtl]
| align="center" | -
| align="center" | 2.184
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastQTL is a QTL mapper Homepage: http://fastqtl.sourceforge.net/ URL: http://fastqtl.sourceforge.net/<br /><br /><br /></div>
|-
| align="center" | [http://cmpg.unibe.ch/software/fastsimcoal2/ fastsimcoal2]
| align="center" | bio
| align="center" | 2.6.0.3, 2.7.0.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure. fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations. Homepage: http://cmpg.unibe.ch/software/fastsimcoal2/ URL: http://cmpg.unibe.ch/software/fastsimcoal2/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.microbesonline.org/fasttree/ fasttree]
| align="center" | bio
| align="center" | 2.1.10
| Documentation: [[FastTree]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. Homepage: http://www.microbesonline.org/fasttree/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://hannonlab.cshl.edu/fastx_toolkit/ fastx-toolkit]
| align="center" | bio
| align="center" | 0.0.14
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Homepage: http://hannonlab.cshl.edu/fastx_toolkit/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://altairhyperworks.com/product/FEKO feko]
| align="center" | phys
| align="center" | 2018
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FEKO is a comprehensive computational electromagnetics (CEM) code used widely in the telecommunications, automobile, space and defense industries. Homepage: https://altairhyperworks.com/product/FEKO Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://www.fftw.org fftw]
| align="center" | math
| align="center" | 3.3.4, 3.3.6, 3.3.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: http://www.fftw.org URL: http://www.fftw.org Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://www.fftw.org fftw-mpi]
| align="center" | math
| align="center" | 2.1.5, 3.3.6, 3.3.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: http://www.fftw.org Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://github.com/rrwick/Filtlong filtlong]
| align="center" | bio
| 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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release flexiblas]
| align="center" | -
| align="center" | 3.0.4
| <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>
|-
| align="center" | [https://www.ansys.com/products/fluids/ansys-fluent fluent]
| align="center" | phys
| 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>
|-
| align="center" | [https://fmriprep.org/ fmriprep]
| align="center" | -
| align="center" | 23.0.2, 23.1.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI). Homepage: https://fmriprep.org/ URL: https://fmriprep.org/<br /><br /><br /></div>
|-
| align="center" | [http://fmtlib.net/ fmt]
| align="center" | -
| align="center" | 5.3.0, 6.1.1, 6.2.1, 7.0.3
| <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>
|-
| align="center" | [https://github.com/ariloytynoja/fpa fpa]
| align="center" | -
| align="center" | nov.23.2016
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FPA the four-point aligner Homepage: https://github.com/ariloytynoja/fpa<br /><br /><br /></div>
|-
| align="center" | [https://sourceforge.net/projects/freepascal/ fpc]
| align="center" | tools
| align="center" | 3.0.0
| <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>
|-
| align="center" | [https://github.com/ekg/freebayes freebayes]
| align="center" | bio
| align="center" | 1.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bayesian haplotype-based polymorphism discovery and genotyping. Homepage: https://github.com/ekg/freebayes Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://freesurfer.net/ freesurfer]
| align="center" | bio
| align="center" | 5.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. Homepage: http://freesurfer.net/ URL: http://freesurfer.net/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.fmrib.ox.ac.uk/fsl/ fsl]
| align="center" | bio
| align="center" | 5.0.11
| <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: http://www.fmrib.ox.ac.uk/fsl/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/ctSkennerton/fxtract fxtract]
| align="center" | -
| align="center" | 2.3
| <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>
|-
| align="center" | [http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2clib]
| align="center" | geo
| align="center" | 1.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder ('C' version). Homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2lib]
| align="center" | geo
| align="center" | 1.4.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library contains GRIB2 encoder/decoder and search/indexing routines. Homepage: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [http://hpc.pnl.gov/globalarrays/ ga]
| align="center" | tools
| align="center" | 5.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency. I8 version. Homepage: http://hpc.pnl.gov/globalarrays/ URL: http://hpc.pnl.gov/globalarrays/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.msg.chem.iastate.edu/GAMESS/GAMESS.html gamess-us]
| align="center" | chem
| align="center" | 20170420-R1, 20180920-R3, 20190630-R1
| 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 Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.opengatecollaboration.org/ gate]
| align="center" | bio
| align="center" | 8.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography Homepage: http://www.opengatecollaboration.org/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk]
| 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
| <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>
|-
| align="center" | [http://www.broadinstitute.org/gatk/ gatk-queue]
| align="center" | bio
| align="center" | 3.8-0
| <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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://molevol.cmima.csic.es/castresana/Gblocks.html gblocks]
| align="center" | -
| align="center" | 0.91b
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Homepage: http://molevol.cmima.csic.es/castresana/Gblocks.html URL: http://molevol.cmima.csic.es/castresana/Gblocks.html<br /><br /><br /></div>
|-
| align="center" | [https://gcc.gnu.org/ gcc]
| 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
| <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>
|-
| align="center" | [http://gcc.gnu.org/ gcc-offload]
| align="center" | -
| align="center" | 9.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Compiler with OpenMP/OpenACC offload support for Nvidia PTX Homepage: http://gcc.gnu.org/ URL: http://gcc.gnu.org/<br /><br /><br /></div>
|-
| align="center" | [http://www.gdal.org/ gdal]
| align="center" | geo
| align="center" | 2.1.3, 2.2.1
| <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/ Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [http://geant4.cern.ch/ geant4]
| align="center" | phys
| align="center" | 10.02.p03, 10.04.p02, 10.05.p01
| <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/ Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [https://geant4.cern.ch/ geant4-data]
| align="center" | -
| align="center" | 10.7.3, 11.1.0
| <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>
|-
| align="center" | [http://geant4.cern.ch/ geant4-seq]
| align="center" | -
| align="center" | 10.02.p03, 10.05.p01
| <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/<br /><br /><br /></div>
|-
| align="center" | [http://trac.osgeo.org/geos geos]
| align="center" | geo
| align="center" | 3.6.1
| <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 Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [https://github.com/gpertea/gffcompare gffcompare]
| align="center" | -
| align="center" | 0.11.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. Homepage: https://github.com/gpertea/gffcompare URL: https://github.com/gpertea/gffcompare<br /><br /><br /></div>
|-
| align="center" | [https://github.com/gpertea/gffread gffread]
| align="center" | -
| align="center" | 0.11.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. Homepage: https://github.com/gpertea/gffread URL: https://github.com/gpertea/gffread<br /><br /><br /></div>
|-
| align="center" | [http://ghostscript.com ghostscript]
| align="center" | -
| align="center" | 9.26
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. Homepage: http://ghostscript.com<br /><br /><br /></div>
|-
| align="center" | [http://git-annex.branchable.com/ git-annex]
| align="center" | tools
| align="center" | 6.20180807, 8.20200810, 10.20221003
| <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>
|-
| align="center" | [https://git-lfs.github.com git-lfs]
| align="center" | -
| align="center" | 2.11.0, 3.3.0
| <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>
|-
| align="center" | [https://www.glfw.org glfw]
| align="center" | -
| align="center" | 3.3.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org<br /><br /><br /></div>
|-
| align="center" | [https://github.com/g-truc/glm glm]
| align="center" | vis
| align="center" | 0.9.7.2, 0.9.9.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. Homepage: https://github.com/g-truc/glm URL: https://github.com/g-truc/glm Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://github.com/cea-hpc/glost glost]
| align="center" | tools
| align="center" | 0.3.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This is GLOST, the Greedy Launcher Of Small Tasks. Homepage: https://github.com/cea-hpc/glost URL: https://github.com/cea-hpc/glost Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.gnu.org/software/glpk/ glpk]
| align="center" | math
| align="center" | 4.61
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. - Homepage: https://www.gnu.org/software/glpk/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://research-pub.gene.com/gmap/ gmap-gsnap]
| align="center" | bio
| align="center" | 2017-04-13
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program - Homepage: http://research-pub.gene.com/gmap/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://gmplib.org/ gmp]
| align="center" | -
| align="center" | 6.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. Homepage: http://gmplib.org/ URL: http://gmplib.org/<br /><br /><br /></div>
|-
| align="center" | [https://www.google.ca/search?q=gmpich gmpich]
| align="center" | -
| align="center" | 2019.05
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: gcc and GFortran based compiler toolchain, including MPICH for MPI support. Homepage: (none)<br /><br /><br /></div>
|-
| align="center" | [http://gnuplot.sourceforge.net/ gnuplot]
| align="center" | vis
| align="center" | 5.2.8
| <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>
|-
| align="center" | [https://www.golang.org go]
| align="center" | tools
| align="center" | 1.10.3, 1.14.1, 1.14.4, 1.18.3, 1.21.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. Homepage: https://www.golang.org URL: https://www.golang.org Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://grackle.readthedocs.io grackle]
| align="center" | phys
| align="center" | 2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Grackle is a chemistry and radiative cooling library for astrophysical simulations and models. Homepage: http://grackle.readthedocs.io Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://www.gromacs.org gromacs]
| align="center" | chem
| align="center" | 4.6.7, 5.0.7, 5.1.4, 2016.3, 2019.2, 2019.3
| 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. simulating the Newtonian equations of motion for systems with hundreds to millions of particles. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.gromacs.org gromacs-plumed]
| align="center" | chem
| align="center" | 2016.3, 2018.1
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version contains the PLUMED patches in order to run metadynamics. - CC-Wiki: GROMACS Homepage: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://www.gnu.org/software/gsl/ gsl]
| align="center" | math
| align="center" | 1.16, 2.2.1, 2.3, 2.5, 2.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. Homepage: https://www.gnu.org/software/gsl/ URL: https://www.gnu.org/software/gsl/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://github.com/gsl-lite/gsl-lite gsl-lite]
| align="center" | -
| align="center" | 0.40.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A single-file header-only version of ISO C++ Guidelines Support Library (GSL) for C++98, C++11, and later Homepage: https://github.com/gsl-lite/gsl-lite URL: https://github.com/gsl-lite/gsl-lite<br /><br /><br /></div>
|-
| align="center" | [https://github.com/google/googletest gtest]
| align="center" | -
| align="center" | 1.10.0
| <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<br /><br /><br /></div>
|-
| align="center" | [https://www.gtk.org/ gtk+3]
| align="center" | tools
| align="center" | 3.20.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GTK+, or the GIMP Toolkit, is a multi-platform toolkit for creating graphical user interfaces. Offering a complete set of widgets, GTK+ is suitable for projects ranging from small one-off tools to complete application suites. Homepage: https://www.gtk.org/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html gtool]
| align="center" | -
| align="center" | 0.7.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. Homepage: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html URL: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html<br /><br /><br /></div>
|-
| align="center" | [http://www.gnu.org/software/guile guile]
| align="center" | tools
| align="center" | 1.8.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. Homepage: http://www.gnu.org/software/guile Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.gurobi.com gurobi]
| align="center" | math
| align="center" | 8.1.1, 9.0.1, 9.0.2, 9.0.3, 9.1.0, 9.1.2, 9.5.0, 9.5.2, 10.0.1, 10.0.2, 10.0.3, 11.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. Homepage: https://www.gurobi.com URL: https://www.gurobi.com Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://www.hdfgroup.org/h4toh5/ h4toh5]
| align="center" | io
| align="center" | 2.2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects. Homepage: http://www.hdfgroup.org/h4toh5/ Keyword:io<br /><br /><br /></div>
|-
| align="center" | [https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html hapgen2]
| align="center" | -
| align="center" | 2.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: 'HAPGEN2' simulates case control datasets at SNP markers. Homepage: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html URL: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html<br /><br /><br /></div>
|-
| align="center" | [https://www.broadinstitute.org/haploview/haploview haploview]
| align="center" | -
| align="center" | 4.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Homepage: https://www.broadinstitute.org/haploview/haploview URL: https://www.broadinstitute.org/haploview/haploview<br /><br /><br /></div>
|-
| align="center" | [http://www.hdfgroup.org/products/hdf4/ hdf]
| align="center" | io
| align="center" | 4.2.12
| <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: http://www.hdfgroup.org/products/hdf4/ Keyword:io<br /><br /><br /></div>
|-
| align="center" | [https://portal.hdfgroup.org/display/support hdf5]
| align="center" | io
| align="center" | 1.8.18, 1.8.20, 1.10.3, 1.10.6
| <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/3.6, python/3.7, python/3.8 Extensions: cached-property-1.5.2, h5py-3.1.0, tables-3.6.1 Keyword:io<br /><br /><br /></div>
|-
| align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi]
| align="center" | io
| align="center" | 1.8.18, 1.10.3, 1.10.6
| <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/3.6, python/3.7, python/3.8 Extensions: cached-property-1.5.2, h5py-3.1.0, tables-3.6.1 Keyword:io<br /><br /><br /></div>
|-
| align="center" | [https://support.hdfgroup.org/products/java/hdfview/ hdfview]
| align="center" | -
| align="center" | 2.14
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDFView is a visual tool for browsing and editing HDF4 and HDF5 files. Homepage: https://support.hdfgroup.org/products/java/hdfview/ URL: https://support.hdfgroup.org/products/java/hdfview/<br /><br /><br /></div>
|-
| align="center" | [https://heasarc.nasa.gov/lheasoft/ heasoft]
| align="center" | phys
| align="center" | 6.26.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A Unified Release of the FTOOLS and XANADU Software Packages XANADU High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis FTOOLS General and mission-specific tools to manipulate FITS files FITSIO Core library responsible for reading and writing FITS files (distributed with FTOOLS) fv General FITS file browser/editor/plotter with a graphical user interface (distributed with FTOOLS) XSTAR Tool for calculating the physical conditions and emission spectra of photoionized gases Homepage: https://heasarc.nasa.gov/lheasoft/ URL: https://heasarc.nasa.gov/lheasoft/ Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [https://github.com/soedinglab/hh-suite hh-suite]
| align="center" | bio
| align="center" | 3.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. Homepage: https://github.com/soedinglab/hh-suite URL: https://github.com/soedinglab/hh-suite Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://ccb.jhu.edu/software/hisat2/index.shtml hisat2]
| align="center" | bio
| align="center" | 2.1.0
| <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>
|-
| align="center" | [http://hmmer.org/ hmmer]
| align="center" | bio
| align="center" | 2.3.2, 3.1b2, 3.2.1
| <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>
|-
| align="center" | [http://www.netlib.org/benchmark/hpl/ hpl]
| align="center" | tools
| align="center" | 2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. Homepage: http://www.netlib.org/benchmark/hpl/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.htslib.org/ htslib]
| align="center" | bio
| align="center" | 1.4, 1.5, 1.9
| <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: http://www.htslib.org/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.open-mpi.org/projects/hwloc/ hwloc]
| align="center" | -
| align="center" | 2.4.0, 2.7.1
| <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>
|-
| align="center" | [http://www.ichthyop.org/ ichthyop]
| align="center" | -
| align="center" | 3.3.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ichthyop is a free Java tool designed to study the effects of physical and biological factors on ichthyoplankton dynamics. It incorporates the most important processes involved in fish early life: spawning, movement, growth, mortality and recruitment. The tool uses as input time series of velocity, temperature and salinity fields archived from ROMS, MARS, NEMO or SYMPHONIE oceanic models (either files or OpenDAP). Homepage: http://www.ichthyop.org/<br /><br /><br /></div>
|-
| align="center" | [https://www.ncbi.nlm.nih.gov/igblast/intro.html igblast]
| align="center" | bio
| align="center" | 1.7.0, 1.16.0, 1.17.0, 1.18.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin variable domain sequences (IgBLAST has recently been extended to perform analysis for T cell receptor (TR) sequences). It uses BLAST search algorithm. Homepage: https://www.ncbi.nlm.nih.gov/igblast/intro.html URL: https://www.ncbi.nlm.nih.gov/igblast/intro.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://igraph.org igraph]
| align="center" | math
| align="center" | 0.7.1
| <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: http://igraph.org Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://www.broadinstitute.org/software/igv/ igv]
| align="center" | -
| align="center" | 2.9.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. Homepage: https://www.broadinstitute.org/software/igv/ URL: https://www.broadinstitute.org/software/igv/<br /><br /><br /></div>
|-
| align="center" | [http://www.imagemagick.org/ imagemagick]
| align="center" | -
| align="center" | 7.0.8-53
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images Homepage: http://www.imagemagick.org/<br /><br /><br /></div>
|-
| align="center" | [https://software.intel.com/en-us/articles/intel-mpi-benchmarks imb]
| align="center" | -
| align="center" | 2019.3
| <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" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html imkl]
| 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
| <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" | mpi
| align="center" | 2017.4.239
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel MPI Library, compatible with MPICH ABI Homepage: http://software.intel.com/en-us/intel-mpi-library/<br /><br /><br /></div>
|-
| align="center" | [http://mathgen.stats.ox.ac.uk/impute/impute_v2.html impute2]
| align="center" | bio
| 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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://jmarchini.org/software/#impute-5 impute5]
| align="center" | -
| align="center" | 1.1.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples. This method continues to refine the observation made in the IMPUTE2 method, that accuracy is optimized via use of a custom subset of haplotypes when imputing each individual. It achieves fast, accurate, and memory-efficient imputation by selecting haplotypes using the Positional Burrows Wheeler Transform (PBWT). By using the PBWT data structure at genotyped markers, IMPUTE 5 identifies locally best matching haplotypes and long identical by state segments. The method then uses the selected haplotypes as conditioning states within the IMPUTE model. IMPUTE5 is up to 30x faster than MINIMAC4 and up to 3x faster than BEAGLE5.1 Homepage: https://jmarchini.org/software/#impute-5 URL: https://jmarchini.org/software/#impute-5<br /><br /><br /></div>
|-
| align="center" | [http://eddylab.org/infernal/ infernal]
| align="center" | bio
| align="center" | 1.0.2, 1.1.2
| <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>
|-
| align="center" | [http://software.intel.com/en-us/intel-inspector-xe inspector]
| align="center" | tools
| align="center" | 2018.3
| <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" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html intel]
| 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
| <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" | -
| align="center" | 2021.2.0
| <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" | mpi
| align="center" | 2018.3.222, 2019.3.199
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel MPI Library, compatible with MPICH ABI Homepage: http://software.intel.com/en-us/intel-mpi-library/<br /><br /><br /></div>
|-
| align="center" | [https://intelxed.github.io/ intelxed]
| align="center" | -
| align="center" | 12.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The X86 Encoder Decoder (XED), is a software library (and associated headers) for encoding and decoding X86 (IA32 and Intel64) instructions. Homepage: https://intelxed.github.io/ URL: https://intelxed.github.io/<br /><br /><br /></div>
|-
| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan]
| align="center" | bio
| align="center" | 5.23-62.0, 5.40-77.0, 5.50-84.0, 5.52-86.0, 5.53-87.0, 5.55-88.0, 5.56-89.0, 5.63-95.0, 5.64-96.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan_data]
| align="center" | -
| align="center" | 5.63-95.0, 5.64-96.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/<br /><br /><br /></div>
|-
| align="center" | [https://software.intel.com/en-us/articles/intel-ipp/ ipp]
| align="center" | tools
| align="center" | 9.0.4, 2017.1.132, 2020.1.217
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. Homepage: https://software.intel.com/en-us/articles/intel-ipp/ URL: https://software.intel.com/en-us/articles/intel-ipp/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://ipython.org/ ipykernel]
| align="center" | -
| 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 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" | -
| align="center" | 2.7, 3.5, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IPython kernelspec for Python 3.11 Homepage: https://ipython.org/ URL: https://ipython.org/<br /><br /><br /></div>
|-
| align="center" | [http://www.iqtree.org/ iq-tree]
| align="center" | bio
| align="center" | 1.5.5, 2.0.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/ URL: http://www.iqtree.org/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://ispc.github.io/ ispc]
| align="center" | -
| align="center" | 1.10.0, 1.13.0, 1.18.0
| <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>
|-
| align="center" | [https://software.intel.com/en-us/intel-trace-analyzer/ itac]
| align="center" | tools
| align="center" | 2018.3.022, 2021.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. Homepage: https://software.intel.com/en-us/intel-trace-analyzer/ URL: https://software.intel.com/en-us/intel-trace-analyzer/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://mcmc-jags.sourceforge.net/ jags]
| align="center" | math
| align="center" | 4.2.0, 4.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation Homepage: http://mcmc-jags.sourceforge.net/ URL: http://mcmc-jags.sourceforge.net/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://www.ece.uvic.ca/~frodo/jasper/ jasper]
| align="center" | vis
| align="center" | 1.900.1, 2.0.16
| <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" | [http://openjdk.java.net java]
| 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
| 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" | [http://www.genome.umd.edu/jellyfish.html jellyfish]
| align="center" | bio
| align="center" | 1.1.11, 2.2.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Homepage: http://www.genome.umd.edu/jellyfish.html URL: http://www.genome.umd.edu/jellyfish.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://julialang.org julia]
| align="center" | tools
| align="center" | 0.5.1, 0.6.0, 1.0.0, 1.0.2, 1.1.0, 1.1.1, 1.2.0, 1.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A high-level, high-performance dynamic language for technical computing. Homepage: http://julialang.org URL: http://julialang.org Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://pachterlab.github.io/kallisto/ kallisto]
| align="center" | bio
| align="center" | 0.44.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. Homepage: http://pachterlab.github.io/kallisto/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://openkim.org/ kim]
| align="center" | chem
| align="center" | 1.8.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenKIM is an online suite of open source tools for molecular simulation of materials. These tools help to make molecular simulation more accessible and more reliable. Within OpenKIM, you will find an online resource for standardized testing and long-term warehousing of interatomic models and data, and an application programming interface (API) standard for coupling atomistic simulation codes and interatomic potential subroutines. Homepage: https://openkim.org/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://bitbucket.org/genomicepidemiology/kma kma]
| align="center" | -
| align="center" | 1.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. Homepage: https://bitbucket.org/genomicepidemiology/kma URL: https://bitbucket.org/genomicepidemiology/kma<br /><br /><br /></div>
|-
| align="center" | [https://www.knime.com/ knime]
| align="center" | -
| align="center" | 4.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: KNIME Analytics Platform is the open source software for creating data science applications and services. KNIME stands for KoNstanz Information MinEr. Homepage: https://www.knime.com/ URL: https://www.knime.com/<br /><br /><br /></div>
|-
| align="center" | [http://ccb.jhu.edu/software/kraken/ kraken]
| align="center" | bio
| align="center" | 0.10.5-beta
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Homepage: http://ccb.jhu.edu/software/kraken/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://lammps.sandia.gov/ lammps]
| align="center" | chem
| align="center" | 20170331
| Documentation: [[LAMMPS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. 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. It can be coupled to various programs. The following packages are not included within this version: GPU, KIM, KOKKOS, MSCG, OPT, USER-INTEL, USER-MISC, USER-OMP, USER-QUIP, USER-VTK Homepage: http://lammps.sandia.gov/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://lammps.sandia.gov/ lammps-omp]
| align="center" | chem
| align="center" | 20170331, 20170811
| Documentation: [[LAMMPS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. 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. It can be coupled to various programs. The following packages are not included within this version: -GPU, -KOKKOS, -MSCG, -USER-INTEL, -USER-QUIP Homepage: http://lammps.sandia.gov/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://lammps.sandia.gov/ lammps-user-intel]
| align="center" | chem
| align="center" | 20170331, 20170811
| Documentation: [[LAMMPS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation. 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. It can be coupled to various programs. The following packages are not included within this version: -GPU, -KOKKOS, -MANYBODY, -MSCG, -QEQ, -USER-ATC, -USER-QUIP Homepage: http://lammps.sandia.gov/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://last.cbrc.jp/ last]
| align="center" | bio
| align="center" | 959
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LAST finds similar regions between sequences. Homepage: http://last.cbrc.jp/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://wiki.dlang.org/LDC ldc]
| align="center" | -
| align="center" | 0.17.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The LLVM-based D Compiler Homepage: https://wiki.dlang.org/LDC URL: https://wiki.dlang.org/LDC<br /><br /><br /></div>
|-
| align="center" | [https://github.com/CDAT/libcdms/ libcdms]
| align="center" | -
| align="center" | 3.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Climate Data Management System Library. Homepage: https://github.com/CDAT/libcdms/ URL: https://github.com/CDAT/libcdms/<br /><br /><br /></div>
|-
| align="center" | [https://jugit.fz-juelich.de/mlz/libcerf libcerf]
| align="center" | math
| align="center" | 1.13
| <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>
|-
| align="center" | [http://www.hyperrealm.com/libconfig/ libconfig]
| align="center" | tools
| align="center" | 1.7.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libconfig is a simple library for processing structured configuration files Homepage: http://www.hyperrealm.com/libconfig/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/CDAT/libdrs/ libdrs]
| align="center" | -
| align="center" | 3.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PCMDI's old DRS format implementation Homepage: https://github.com/CDAT/libdrs/ URL: https://github.com/CDAT/libdrs/<br /><br /><br /></div>
|-
| align="center" | [https://libevent.org/ libevent]
| align="center" | -
| align="center" | 2.1.11
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. Homepage: https://libevent.org/ URL: https://libevent.org/<br /><br /><br /></div>
|-
| align="center" | [https://ofiwg.github.io/libfabric/ libfabric]
| align="center" | -
| align="center" | 1.10.1
| <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://sourceware.org/libffi/ libffi]
| align="center" | -
| align="center" | 3.3
| <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" | vis
| align="center" | 2.2.5, 2.3.0
| <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://directory.fsf.org/wiki/Libgeotiff libgeotiff]
| align="center" | -
| align="center" | 1.5.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Library for reading and writing coordinate system information from/to GeoTIFF files Homepage: https://directory.fsf.org/wiki/Libgeotiff URL: https://directory.fsf.org/wiki/Libgeotiff<br /><br /><br /></div>
|-
| align="center" | [http://deeplearning.net/software/libgpuarray libgpuarray]
| align="center" | math
| align="center" | 0.6.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Homepage: http://deeplearning.net/software/libgpuarray Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://hannonlab.cshl.edu/fastx_toolkit/ libgtextutils]
| align="center" | bio
| 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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://libharu.org/ libharu]
| align="center" | -
| 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: http://libharu.org/ URL: http://libharu.org/<br /><br /><br /></div>
|-
| align="center" | [https://github.com/evaleev/libint libint]
| align="center" | chem
| align="center" | 1.1.6, 2.2.0
| <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://github.com/evaleev/libint Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://github.com/libMesh/libmesh libmesh]
| align="center" | math
| align="center" | 1.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The libMesh library provides a framework for the numerical simulation of partial differential equations using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist to focus on the physics they are modeling. Homepage: https://github.com/libMesh/libmesh Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://libqglviewer.com/ libqglviewer]
| align="center" | -
| align="center" | 2.7.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers. Homepage: http://libqglviewer.com/ URL: http://libqglviewer.com/<br /><br /><br /></div>
|-
| align="center" | [https://doc.libsodium.org/ libsodium]
| align="center" | -
| align="center" | 1.0.18
| <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" | phys
| align="center" | 1.8.5
| <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>
|-
| align="center" | [https://www.csie.ntu.edu.tw/~cjlin/libsvm/ libsvm]
| align="center" | -
| align="center" | 3.24
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). Homepage: https://www.csie.ntu.edu.tw/~cjlin/libsvm/ URL: https://www.csie.ntu.edu.tw/~cjlin/libsvm/<br /><br /><br /></div>
|-
| align="center" | [https://www.tddft.org/programs/libxc libxc]
| align="center" | chem
| align="center" | 3.0.0, 4.2.1, 4.2.3, 4.3.4
| <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://www.tddft.org/programs/libxc URL: https://www.tddft.org/programs/libxc Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://github.com/hfp/libxsmm libxsmm]
| align="center" | math
| align="center" | 1.8
| <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 Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://github.com/limix/liknorm liknorm]
| align="center" | -
| align="center" | 1.5.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C library for computing moments of the product of an exponential-family likelihood with a Normal distribution. Homepage: https://github.com/limix/liknorm URL: https://github.com/limix/liknorm<br /><br /><br /></div>
|-
| align="center" | [https://github.com/limix/bgen limix-bgen]
| align="center" | -
| align="center" | 3.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. Homepage: https://github.com/limix/bgen URL: https://github.com/limix/bgen<br /><br /><br /></div>
|-
| align="center" | [http://www.littlecms.com/ littlecms]
| align="center" | -
| align="center" | 2.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. Homepage: http://www.littlecms.com/<br /><br /><br /></div>
|-
| align="center" | [https://lldb.llvm.org/ lldb]
| align="center" | -
| align="center" | 11.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The debugger component of the LLVM project Homepage: https://lldb.llvm.org/ URL: https://lldb.llvm.org/<br /><br /><br /></div>
|-
| align="center" | [https://llvm.org/ llvm]
| align="center" | tools
| align="center" | 6.0.1, 7.0.0, 8.0.1, 9.0.1
| <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" | -
| align="center" | 0.9.24
| <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>
|-
| align="center" | [https://sourceforge.net/projects/lpsolve/ lpsolve]
| align="center" | math
| 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/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://www.lstc.com/products/ls-opt ls-opt]
| align="center" | phys
| align="center" | 5.2.1, 7.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LS-OPT is a standalone Design Optimization and Probabilistic Analysis package with an interface to LS-DYNA. Homepage: http://www.lstc.com/products/ls-opt URL: http://www.lstc.com/products/ls-opt Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://lstc.com/products/ls-prepost ls-prepost]
| align="center" | -
| align="center" | 4.7.8, 4.7.13, 4.8.11, 4.9.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA. Homepage: http://lstc.com/products/ls-prepost URL: http://lstc.com/products/ls-prepost<br /><br /><br /></div>
|-
| align="center" | [https://github.com/arq5x/lumpy-sv lumpy]
| align="center" | bio
| 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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://csg.sph.umich.edu/abecasis/MACH/ mach]
| align="center" | bio
| align="center" | 1.0.18
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. - Homepage: http://csg.sph.umich.edu/abecasis/MACH/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://mafft.cbrc.jp/alignment/software/ mafft]
| align="center" | bio
| align="center" | 7.310
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of &lt; ~200 sequences), FFT-NS-2 (fast; for alignment of &lt; ~10,000 sequences), etc. Homepage: http://mafft.cbrc.jp/alignment/software/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://mafft.cbrc.jp/alignment/software/source.html mafft-mpi]
| align="center" | -
| align="center" | 7.471
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of &lt;200 sequences), FFT-NS-2 (fast; for alignment of &lt;30,000 sequences), etc. Homepage: https://mafft.cbrc.jp/alignment/software/source.html URL: https://mafft.cbrc.jp/alignment/software/source.html<br /><br /><br /></div>
|-
| align="center" | [http://icl.cs.utk.edu/magma/ magma]
| align="center" | math
| align="center" | 2.2.0
| <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: http://icl.cs.utk.edu/magma/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://www.gnu.org/software/make/make.html make]
| align="center" | tools
| align="center" | 3.82
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: make-3.82: GNU version of make utility Homepage: http://www.gnu.org/software/make/make.html Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.yandell-lab.org/software/maker.html maker]
| align="center" | bio
| align="center" | 2.31.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. Homepage: http://www.yandell-lab.org/software/maker.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/Illumina/manta manta]
| align="center" | bio
| align="center" | 1.2.2
| <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>
|-
| align="center" | [https://docs.computecanada.ca/wiki/Database_servers. mariadb]
| align="center" | tools
| align="center" | 10.1.21, 10.4.11
| <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/ Extensions: DBD::mysql-4.050, Devel::CheckLib-1.13, IO::CaptureOutput-1.1104 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://downloads.mariadb.org/connector-c/ mariadb-connector-c]
| align="center" | -
| align="center" | 3.1.7
| <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>
|-
| align="center" | [http://sourceforge.net/projects/matio/ matio]
| align="center" | io
| align="center" | 1.5.2
| <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: http://sourceforge.net/projects/matio/ Keyword:io<br /><br /><br /></div>
|-
| align="center" | [http://www.mathworks.com/products/matlab matlab]
| 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
| 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" | tools
| align="center" | 3.5.0, 3.6.3
| <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>
|-
| align="center" | [https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html maxbin]
| align="center" | bio
| align="center" | 2.2.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users can use MEGAN or similar software on MaxBin bins to find the taxonomy of each bin after the binning process is finished. Homepage: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr]
| align="center" | tools
| align="center" | R2013a, R2013b, R2014a, R2014b, R2015a, R2015b, R2016a, R2016b, R2017a, R2017b, R2018a, R2018b, R2019a, R2019b, R2020a, R2020b, R2021b, R2022b
| Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: https://www.mathworks.com/products/compiler/mcr/ URL: https://www.mathworks.com/products/compiler/mcr/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/voutcn/megahit megahit]
| align="center" | bio
| align="center" | 1.1.1
| <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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://meme-suite.org meme]
| align="center" | -
| align="center" | 5.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MEME Suite allows you to: - discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, - search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, - compare a motif to all motifs in a database of motifs, - associate motifs with Gene Ontology terms via their putative target genes, - analyse motif enrichment using SpaMo or CentriMo. Homepage: http://meme-suite.org<br /><br /><br /></div>
|-
| align="center" | [http://jgi.doe.gov/data-and-tools/meraculous/ meraculous]
| align="center" | bio
| align="center" | 2.2.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Distributed and scalable assembler for eukaryotic genomes. Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on commodity clusters in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures. Homepage: http://jgi.doe.gov/data-and-tools/meraculous/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.mesa3d.org/ mesa]
| align="center" | vis
| align="center" | 18.3.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Homepage: https://www.mesa3d.org/ URL: https://www.mesa3d.org/ Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://software.sandia.gov/mesquite/ mesquite]
| align="center" | math
| 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/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://docs.computecanada.ca/wiki/META_package_for_serial_farming meta-farm]
| align="center" | -
| align="center" | 1.0.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Meta-farm is a suite of scripts designed in-house to fully automate throughput computing (running a large number of related serial/parallel/GPU jobs - so called farming). Homepage: https://docs.computecanada.ca/wiki/META_package_for_serial_farming URL: https://docs.computecanada.ca/wiki/META_package_for_serial_farming<br /><br /><br /></div>
|-
| align="center" | [https://bitbucket.org/berkeleylab/metabat metabat]
| align="center" | bio
| align="center" | 2.12.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data Homepage: https://bitbucket.org/berkeleylab/metabat Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://metagene.nig.ac.jp/ metageneannotator]
| align="center" | -
| align="center" | 20080819
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MetaGeneAnnotator is a gene-finding program for prokaryote and phage. Homepage: http://metagene.nig.ac.jp/ URL: http://metagene.nig.ac.jp/<br /><br /><br /></div>
|-
| align="center" | [http://www.sph.umich.edu/csg/abecasis/metal/ metal]
| align="center" | bio
| 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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://bitbucket.org/biobakery/metaphlan2 metaphlan]
| align="center" | bio
| align="center" | 2.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. Homepage: https://bitbucket.org/biobakery/metaphlan2 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/metis/overview metis]
| align="center" | math
| align="center" | 4.0.3, 5.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://github.com/codeandkey/mii mii]
| align="center" | -
| align="center" | 1.1.1, 1.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A smart search engine for module environments. Homepage: https://github.com/codeandkey/mii URL: https://github.com/codeandkey/mii<br /><br /><br /></div>
|-
| align="center" | [http://minia.genouest.org/ minia]
| align="center" | bio
| align="center" | 2.0.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minia is a short-read assembler based on a de Bruijn graph Homepage: http://minia.genouest.org/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://genome.sph.umich.edu/wiki/Minimac2 minimac2]
| align="center" | bio
| align="center" | 2014.9.15
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: minimac2 is an improved version of Minimac. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. - Homepage: http://genome.sph.umich.edu/wiki/Minimac2 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://genome.sph.umich.edu/wiki/Minimac3 minimac3]
| align="center" | bio
| align="center" | 2.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. - Homepage: http://genome.sph.umich.edu/wiki/Minimac3 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://mixcr.readthedocs.io/en/latest/quickstart.html mixcr]
| align="center" | bio
| align="center" | 2.1.5, 2.1.10, 3.0.13, 4.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MiXCR is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments. Homepage: http://mixcr.readthedocs.io/en/latest/quickstart.html URL: http://mixcr.readthedocs.io/en/latest/quickstart.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.cmbi.ru.nl/molden/ molden]
| align="center" | chem
| align="center" | 5.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac Homepage: http://www.cmbi.ru.nl/molden/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.mono-project.com/ mono]
| align="center" | tools
| align="center" | 4.6.2.7, 5.4.0.56, 5.16.0.179
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. Homepage: http://www.mono-project.com/ URL: http://www.mono-project.com/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.mothur.org/ mothur]
| align="center" | bio
| align="center" | 1.39.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Homepage: http://www.mothur.org/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/jmp75/MPI.NET mpi.net]
| align="center" | mpi
| align="center" | 13-08-2017
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI) for Microsoft's .NET environment. Homepage: https://github.com/jmp75/MPI.NET Keyword:mpi<br /><br /><br /></div>
|-
| align="center" | [https://bitbucket.org/mpi4py/mpi4py mpi4py]
| align="center" | tools
| align="center" | 3.0.0, 3.0.3, 3.1.3
| <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/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.mpich.org/ mpich]
| align="center" | -
| align="center" | 3.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). Homepage: http://www.mpich.org/<br /><br /><br /></div>
|-
| align="center" | [http://mrbayes.csit.fsu.edu mrbayes]
| align="center" | bio
| align="center" | 3.2.6
| <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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://sobereva.com/multiwfn/ multiwfn]
| align="center" | chem
| align="center" | 3.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A multifunctional wavefunction analyzer. Homepage: http://sobereva.com/multiwfn/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://mummer.sourceforge.net/ mummer]
| align="center" | bio
| 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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://mummer.sourceforge.net/ mummer-64bit]
| align="center" | bio
| align="center" | 3.23
| <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" | [http://graal.ens-lyon.fr/MUMPS/ mumps-metis]
| align="center" | tools
| align="center" | 5.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A parallel sparse direct solver Homepage: http://graal.ens-lyon.fr/MUMPS/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://graal.ens-lyon.fr/MUMPS/ mumps-parmetis]
| align="center" | tools
| align="center" | 5.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A parallel sparse direct solver Homepage: http://graal.ens-lyon.fr/MUMPS/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.mysql.com/ mysql]
| align="center" | tools
| align="center" | 5.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MySQL is (as of March 2014) the world's second most widely used open-source relational database management system (RDBMS). Homepage: http://www.mysql.com/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-mpi]
| align="center" | chem
| align="center" | 2.12
| Documentation: [[NAMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-multicore]
| align="center" | chem
| align="center" | 2.12
| Documentation: [[NAMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-verbs]
| align="center" | chem
| align="center" | 2.12
| Documentation: [[NAMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/namd/ namd-verbs-smp]
| align="center" | chem
| align="center" | 2.12
| Documentation: [[NAMD]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://github.com/jlblancoc/nanoflann nanoflann]
| align="center" | -
| align="center" | 1.3.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies Homepage: https://github.com/jlblancoc/nanoflann URL: https://github.com/jlblancoc/nanoflann<br /><br /><br /></div>
|-
| align="center" | [https://developer.nvidia.com/nccl nccl]
| align="center" | tools
| align="center" | 2.7.8, 2.8.4, 2.11.4
| <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>
|-
| align="center" | [http://www.ncl.ucar.edu ncl]
| align="center" | vis
| align="center" | 6.4.0
| <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 Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://nco.sourceforge.net nco]
| align="center" | io
| align="center" | 4.6.6
| <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: http://nco.sourceforge.net Keyword:io<br /><br /><br /></div>
|-
| align="center" | [http://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview]
| align="center" | vis
| align="center" | 2.1.7
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. Homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://www.nektar.info/ nektar++]
| align="center" | math
| align="center" | 4.4.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. Homepage: https://www.nektar.info/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf]
| align="center" | io
| align="center" | 4.4.1.1, 4.6.1, 4.7.4
| <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" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++]
| align="center" | io
| 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/ Keyword:io<br /><br /><br /></div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++-mpi]
| align="center" | io
| 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/ Keyword:io<br /><br /><br /></div>
|-
| align="center" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++4-mpi]
| align="center" | io
| align="center" | 4.3.0
| <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" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran]
| align="center" | io
| align="center" | 4.4.4
| <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" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran-mpi]
| align="center" | io
| align="center" | 4.4.4, 4.5.1
| <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: http://www.unidata.ucar.edu/software/netcdf/ URL: http://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" | io
| align="center" | 4.1.3, 4.4.1.1, 4.6.1, 4.7.4
| <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" | [http://www.lysator.liu.se/~nisse/nettle/ nettle]
| align="center" | -
| align="center" | 3.3
| <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" | [http://python.org/ networkx]
| align="center" | tools
| align="center" | 1.1, 2.1
| <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" | [https://www.nextflow.io nextflow]
| 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
| <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>
|-
| align="center" | [http://cibiv.github.io/NextGenMap/ nextgenmap]
| align="center" | bio
| align="center" | 0.5.0, 0.5.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NextGenMap (NGM) is a flexible and fast read mapping program that is more than twice as fast as BWA, while achieving a mapping sensitivity similar to Stampy or Bowtie2. Homepage: http://cibiv.github.io/NextGenMap/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/nextstrain/cli/tree/3.1.0 nextstrain.cli]
| align="center" | -
| align="center" | 3.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This is the source code repository for a program called nextstrain, the Nextstrain command-line interface (CLI). It aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch. Homepage: https://github.com/nextstrain/cli/tree/3.1.0 URL: https://github.com/nextstrain/cli/tree/3.1.0<br /><br /><br /></div>
|-
| align="center" | [https://github.com/mfumagalli/ngsTools ngstools]
| align="center" | bio
| align="center" | 1.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data. An application note illustrating its application has published (Fumagalli et al., 2014). Homepage: https://github.com/mfumagalli/ngsTools Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://ninja-build.org/ ninja]
| align="center" | -
| align="center" | 1.9.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ninja is a small build system with a focus on speed. Homepage: https://ninja-build.org/ URL: https://ninja-build.org/<br /><br /><br /></div>
|-
| align="center" | [https://github.com/TravisWheelerLab/NINJA ninja-phylogenetics]
| align="center" | -
| align="center" | 0.97-cluster_only
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nearly Infinite Neighbor Joining Application Compute correct neighbor-joining phylogenies for inputs of more than 10,000 sequences. This is a C++/SSE port of the original Java code described in: Wheeler, T.J. 2009. Large-scale neighbor-joining with NINJA. In S.L. Salzberg and T. Warnow (Eds.), Proceedings of the 9th Workshop on Algorithms in Bioinformatics. WABI 2009, pp. 375-389. Springer, Berlin. (LNCS webpage,preprint) The Java version of NINJA was the fastest available tool computing neighbor-joining phylogenies ( 10x faster than the fastest implemenation of the canonical neighbor-joining algorithm - QuickTree ) at the time of it's release. In addition to generating phylogenies, Ninja can be used to output pairwise distances using several common sequence distance measures, and cluster sequences using a nearest-neighbor approach. Homepage: https://github.com/TravisWheelerLab/NINJA URL: https://github.com/TravisWheelerLab/NINJA<br /><br /><br /></div>
|-
| align="center" | [http://ab-initio.mit.edu/wiki/index.php/NLopt nlopt]
| align="center" | math
| align="center" | 2.4.2
| <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 Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://nodejs.org nodejs]
| align="center" | tools
| align="center" | 11.1.0
| <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: http://nodejs.org Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR nspr]
| align="center" | -
| align="center" | 4.21, 4.25
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR<br /><br /><br /></div>
|-
| align="center" | [https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS nss]
| align="center" | -
| align="center" | 3.45, 3.51
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS URL: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS<br /><br /><br /></div>
|-
| align="center" | [http://www.shoup.net/ntl/ ntl]
| align="center" | math
| align="center" | 11.3.0, 11.4.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields. Homepage: http://www.shoup.net/ntl/ URL: http://www.shoup.net/ntl/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://developer.nvidia.com/hpc-sdk/ nvhpc]
| align="center" | tools
| align="center" | 20.7, 22.1, 22.7, 23.7
| <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>
|-
| align="center" | [http://www.nwchem-sw.org nwchem]
| align="center" | chem
| align="center" | 6.6.revision27746
| <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 Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.oasys-software.com/dyna/en/ oasys-ls-dyna]
| align="center" | phys
| align="center" | 14.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Oasys Suite of software, exclusively written for LS-DYNA, is at the leading edge of the pre- and post-processing markets and is used worldwide by many of the largest LS-DYNA customers. Homepage: http://www.oasys-software.com/dyna/en/ Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://www.gnu.org/software/octave/ octave]
| align="center" | tools
| align="center" | 4.2.1
| <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/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page octopus]
| align="center" | chem
| align="center" | 8.4, 9.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page URL: http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://openbabel.org openbabel]
| align="center" | chem
| align="center" | 2.4.1
| <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: http://openbabel.org Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://xianyi.github.com/OpenBLAS/ openblas]
| align="center" | math
| align="center" | 0.2.20, 0.3.4, 0.3.17
| <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>
|-
| align="center" | [https://github.com/sourceryinstitute/opencoarrays opencoarrays]
| align="center" | -
| align="center" | 2.9.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenCoarrays is an open-source software project that supports the coarray Fortran (CAF) parallel programming features of the Fortran 2008 standard and several features proposed for Fortran 2015 in the draft Technical Specification TS 18508 Additional Parallel Features in Fortran. Homepage: https://github.com/sourceryinstitute/opencoarrays URL: https://github.com/sourceryinstitute/opencoarrays<br /><br /><br /></div>
|-
| align="center" | [http://opencolorio.org/ opencolorio]
| align="center" | vis
| align="center" | 1.0.9
| <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/ Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://opencv.org/ opencv]
| align="center" | vis
| align="center" | 2.4.13.3, 3.3.0
| <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/ Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://www.openexr.com/ openexr]
| align="center" | vis
| align="center" | 2.2.1, 2.5.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light and Magic for use in computer imaging applications Homepage: https://www.openexr.com/ URL: https://www.openexr.com/ Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://www.openfoam.com/ openfoam]
| align="center" | phys
| align="center" | 2.2.2, 2.3.1, 2.4.0, 3.0.1, 4.1, 5.0, 6.20180813, 7, 8, v1812, v1906, v1912, v2012
| 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" | phys
| align="center" | 4.0
| <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: http://www.extend-project.de/ Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [https://openimageio.org/ openimageio]
| align="center" | vis
| align="center" | 1.8.7, 2.1.17.0
| <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/ Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://simtk.org/home/openmm openmm]
| align="center" | chem
| align="center" | 7.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. Homepage: https://simtk.org/home/openmm Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://gitlab.com/Molcas/OpenMolcas openmolcas]
| align="center" | chem
| align="center" | 20.07
| <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>
|-
| align="center" | [https://www.open-mpi.org/ openmpi]
| align="center" | mpi
| align="center" | 1.6.5, 1.8.8, 2.0.2, 2.1.1, 3.1.2, 4.0.1, 4.0.3
| <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>
|-
| align="center" | [http://code.google.com/p/openpgm/ openpgm]
| align="center" | tools
| 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: http://code.google.com/p/openpgm/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/OpenRefine/OpenRefine openrefine]
| align="center" | -
| align="center" | 3.3, 3.4.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web. Homepage: https://github.com/OpenRefine/OpenRefine URL: https://github.com/OpenRefine/OpenRefine<br /><br /><br /></div>
|-
| align="center" | [http://opensees.berkeley.edu/ opensees]
| align="center" | -
| align="center" | 3.0.0, 3.0.2
| <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/<br /><br /><br /></div>
|-
| align="center" | [https://github.com/AcademySoftwareFoundation/openvdb openvdb]
| align="center" | -
| align="center" | 7.0.0
| <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>
|-
| align="center" | [https://github.com/OpenVKL/openvkl openvkl]
| align="center" | -
| align="center" | 0.10.0
| <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>
|-
| align="center" | [https://developer.nvidia.com/optix optix]
| align="center" | -
| align="center" | 6.5.0, 7.7.0
| <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>
|-
| align="center" | [http://cec.mpg.de/forum/ orca]
| align="center" | chem
| align="center" | 3.0.3, 4.0.0.2, 4.0.1.2, 4.1.2, 4.2.0
| Documentation: [[ORCA]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Homepage: http://cec.mpg.de/forum/ URL: http://cec.mpg.de/forum/ Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://github.com/wwood/OrfM orfm]
| align="center" | -
| align="center" | 0.7.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences. Homepage: https://github.com/wwood/OrfM<br /><br /><br /></div>
|-
| align="center" | [http://orthomcl.org/ orthomcl]
| align="center" | bio
| 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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/imageworks/OpenShadingLanguage osl]
| align="center" | vis
| align="center" | 1.9.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Advanced shading language for production GI renderers Homepage: https://github.com/imageworks/OpenShadingLanguage Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://github.com/ospray/ospray ospray]
| align="center" | -
| align="center" | 1.8.5
| <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>
|-
| align="center" | [http://mvapich.cse.ohio-state.edu/benchmarks/ osu-micro-benchmarks]
| align="center" | tools
| align="center" | 5.3.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OSU Micro-Benchmarks Homepage: http://mvapich.cse.ohio-state.edu/benchmarks/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.ovito.org ovito]
| align="center" | -
| align="center" | 3.3.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. It helps scientists gain better insights into materials phenomena and physical processes. The program is freely available for all major platforms under an open source license. It has served in a growing number of computational simulation studies as a powerful tool to analyze, understand and illustrate simulation results. Homepage: https://www.ovito.org URL: https://www.ovito.org<br /><br /><br /></div>
|-
| align="center" | [http://www.p4est.org/ p4est]
| align="center" | math
| align="center" | 1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The p4est software library enables the dynamic management of a collection of adaptive octrees, conveniently called a forest of octrees. p4est is designed to work in parallel and scales to hundreds of thousands of processor cores. It is free software released under GNU General Public Licence version 2, or (at your option) any later version. Homepage: http://www.p4est.org/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://www.google.ca/search?q=panther panther]
| align="center" | -
| align="center" | 14.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Panther is the database part of InterProScan software. It contains only data. Homepage: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/ URL: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/<br /><br /><br /></div>
|-
| align="center" | [http://icl.cs.utk.edu/projects/papi/ papi]
| align="center" | tools
| align="center" | 5.6.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. Homepage: http://icl.cs.utk.edu/projects/papi/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://developer.nvidia.com/nvidia-parabricks parabricks]
| align="center" | -
| align="center" | 2.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Analyzing genomic data is computationally intensive. Time and cost are significant barriers to using genomics data for precision medicine. The NVIDIA Parabricks Genomics Analysis Toolkit breaks down those barriers, providing GPU-accelerated genomic analysis. Data that once took days to analyze can now be done in under an hour. Homepage: https://developer.nvidia.com/nvidia-parabricks URL: https://developer.nvidia.com/nvidia-parabricks<br /><br /><br /></div>
|-
| align="center" | [http://savannah.gnu.org/projects/parallel/ parallel]
| align="center" | tools
| align="center" | 20160722
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: parallel: Build and execute shell commands in parallel Homepage: http://savannah.gnu.org/projects/parallel/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.paraview.org paraview]
| align="center" | vis
| align="center" | 5.3.0, 5.5.2, 5.8.0
| 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/3.6, python/3.7, python/3.8 Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://www.paraview.org paraview-offscreen]
| align="center" | vis
| align="center" | 5.3.0
| Documentation: [[Visualization]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://www.paraview.org paraview-offscreen-gpu]
| align="center" | vis
| align="center" | 5.4.0
| Documentation: [[Visualization]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview parmetis]
| align="center" | math
| 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 Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://www-users.cs.umn.edu/~moulitsa/software.html parmgridgen]
| align="center" | math
| align="center" | 1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. Homepage: http://www-users.cs.umn.edu/~moulitsa/software.html Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://pointclouds.org/ pcl]
| align="center" | math
| align="center" | 1.8.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing. Homepage: http://pointclouds.org/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://www.pcre.org/ pcre]
| align="center" | -
| align="center" | 8.39, 8.44
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/<br /><br /><br /></div>
|-
| align="center" | [https://www.pcre.org/ pcre2]
| align="center" | -
| align="center" | 10.31, 10.34
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. Homepage: https://www.pcre.org/ URL: https://www.pcre.org/<br /><br /><br /></div>
|-
| align="center" | [https://www.cs.uoregon.edu/research/pdt/ pdt]
| align="center" | -
| align="center" | 3.25
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. Homepage: https://www.cs.uoregon.edu/research/pdt/ URL: https://www.cs.uoregon.edu/research/pdt/<br /><br /><br /></div>
|-
| align="center" | [http://sco.h-its.org/exelixis/web/software/pear/ pear]
| align="center" | bio
| align="center" | 0.9.10
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. Homepage: http://sco.h-its.org/exelixis/web/software/pear/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://penncnv.openbioinformatics.org/en/latest/ penncnv]
| align="center" | bio
| align="center" | 1.0.4, 1.0.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. Homepage: http://penncnv.openbioinformatics.org/en/latest/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.perl.org/ perl]
| align="center" | tools
| align="center" | 5.16.3, 5.22.2, 5.22.4, 5.30.2
| 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>
|-
| align="center" | [https://metacpan.org/pod/Perl4::CoreLibs perl4-corelibs]
| align="center" | tools
| align="center" | 0.003
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Libraries historically supplied with Perl 4 Homepage: https://metacpan.org/pod/Perl4::CoreLibs Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc]
| align="center" | tools
| align="center" | 3.7.5, 3.8.2, 3.9.0, 3.10.2, 3.11.3
| <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>
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc-64bits]
| align="center" | tools
| align="center" | 3.7.5
| <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 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.mcs.anl.gov/petsc petsc-complex]
| align="center" | tools
| align="center" | 3.9.0, 3.10.4, 3.11.3
| <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>
|-
| align="center" | [https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en pfft]
| align="center" | math
| align="center" | 1.0.8-alpha
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PFFT is a software library for computing massively parallel, fast Fourier transformations on distributed memory architectures. PFFT can be understood as a generalization of FFTW-MPI to multidimensional data decomposition. Homepage: https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software.php.en Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://www.pgroup.com/ pgi]
| align="center" | tools
| align="center" | 13.10, 16.9, 17.3, 19.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: C, C++ and Fortran compilers from The Portland Group - PGI Homepage: http://www.pgroup.com/ URL: http://www.pgroup.com/<br /><br /><br /></div>
|-
| align="center" | [http://samtools.github.io/hts-specs) picard]
| 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
| <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>
|-
| align="center" | [https://github.com/broadinstitute/pilon pilon]
| align="center" | bio
| 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 Homepage: https://github.com/broadinstitute/pilon URL: https://github.com/broadinstitute/pilon Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.well.ox.ac.uk/platypus platypus]
| align="center" | bio
| align="center" | 0.8.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. Homepage: http://www.well.ox.ac.uk/platypus Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink]
| 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, 2.00-10252019-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>
|-
| align="center" | [http://www.plumed-code.org plumed]
| align="center" | chem
| align="center" | 2.3.0, 2.3.2, 2.4.2
| <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: http://www.plumed-code.org Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://pmix.org/ pmix]
| align="center" | -
| align="center" | 1.2.5
| <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>
|-
| align="center" | [https://trac.mcs.anl.gov/projects/parallel-netcdf pnetcdf]
| align="center" | io
| align="center" | 1.8.1
| <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 Keyword:io<br /><br /><br /></div>
|-
| align="center" | [https://podman.io podman]
| align="center" | -
| align="center" | 4.1.1, 4.5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Podman is a daemonless container engine for developing, managing, and running OCI Containers on your Linux System. Homepage: https://podman.io URL: https://podman.io<br /><br /><br /></div>
|-
| align="center" | [https://www.postgresql.org/ postgresql]
| align="center" | tools
| align="center" | 9.6.6, 10.2, 11.6, 12.1
| <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/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://matsen.fhcrc.org/pplacer/ pplacer]
| align="center" | bio
| align="center" | 1.1.alpha19
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. Homepage: http://matsen.fhcrc.org/pplacer/ URL: http://matsen.fhcrc.org/pplacer/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.cs.wm.edu/~andreas/software/ primme]
| align="center" | -
| align="center" | 3.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PRIMME, pronounced as prime, is a high-performance library for computing a few eigenvalues/eigenvectors, and singular values/vectors. PRIMME is especially optimized for large, difficult problems. Real symmetric and complex Hermitian problems, standard A x = \lambda x and generalized A x = \lambda B x, are supported. Besides, standard eigenvalue problems with a normal matrix are supported. It can find largest, smallest, or interior singular/eigenvalues, and can use preconditioning to accelerate convergence. Homepage: http://www.cs.wm.edu/~andreas/software/ URL: http://www.cs.wm.edu/~andreas/software/<br /><br /><br /></div>
|-
| align="center" | [http://prinseq.sourceforge.net prinseq]
| align="center" | bio
| align="center" | 0.20.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A bioinformatics tool to PRe-process and show INformation of SEQuence data. Homepage: http://prinseq.sourceforge.net Extensions: Cairo-1.106, Contextual::Return-0.004008, Digest::MD5-2.54, ExtUtils::Depends-0.405, ExtUtils::PkgConfig-1.15, File::Spec-3.62, File::Temp-0.2304, Getopt::Long-2.48, JSON-2.90, Math::Cephes::Matrix-0.5304, Math::MatrixReal-2.12, MIME::Base64-3.15, Pod::Usage-1.68, Statistics::PCA-0.0.1, Text::SimpleTable-2.03, Want-0.26 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://sourceforge.net/projects/probmask/ probmask]
| align="center" | -
| align="center" | 2011.12
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Probmask (ZORRO) is a probabilistic alignment masking program Homepage: https://sourceforge.net/projects/probmask/<br /><br /><br /></div>
|-
| align="center" | [http://prodigal.ornl.gov/ prodigal]
| align="center" | bio
| align="center" | 2.6.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Homepage: http://prodigal.ornl.gov/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://proj.org proj]
| align="center" | geo
| align="center" | 4.9.3, 6.0.0, 6.3.0, 7.0.0
| <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 Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [https://github.com/google/protobuf/ protobuf]
| align="center" | tools
| align="center" | 3.3.0, 3.6.1, 3.7.1, 3.9.1, 3.11.1
| <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>
|-
| align="center" | [https://pypy.org/index.html pypy]
| align="center" | tools
| align="center" | 5.8.0, 7.3.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PyPy is a fast, compliant alternative implementation of the Python language (2.7.13 and 3.5.3). Homepage: https://pypy.org/index.html URL: https://pypy.org/index.html Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://pytest.org pytest]
| align="center" | -
| 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, 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" | 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
| 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>
|-
| align="center" | [http://python.org/ python-build-bundle]
| align="center" | -
| 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>
|-
| align="center" | [https://bitbucket.org/mpi4py/mpi4py python27-mpi4py]
| align="center" | tools
| align="center" | 2.0.0
| <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 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://python.org/ python27-scipy-stack]
| align="center" | math
| align="center" | 2017a
| <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/ Extensions: arff-2.1.0, backports.shutil_get_terminal_size-1.0.0, backports_abc-0.4, bitstring-3.1.5, blist-1.3.6, certifi-2016.8.8, cryptography-1.7.1, Cycler-0.10.0, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.10, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, functools32-3.2.3-2, ipykernel-4.4.1, ipython-5.1.0, ipython_genutils-0.1.0, ipywidgets-5.2.2, Jinja2-2.8, jsonschema-2.5.1, jupyter_client-4.3.0, jupyter_core-4.1.1, lockfile-0.12.2, MarkupSafe-0.23, matplotlib-1.5.3, mistune-0.7.3, mock-2.0.0, mpmath-0.19, nbformat-4.1.0, netaddr-0.7.18, netifaces-0.10.5, nose-1.3.7, notebook-4.2.2, numpy-1.12.0, pandas-0.19.2, paramiko-2.1.1, path.py-10.0, pathlib2-2.1.0, paycheck-1.0.2, pbr-1.10.0, pexpect-4.2.0, pickleshare-0.7.4, prompt_toolkit-1.0.9, ptyprocess-0.5.1, pycrypto-2.6.1, Pygments-2.1.3, pyparsing-2.1.10, pysqlite-2.8.3, pytz-2016.10, PyZMQ-16.0.2, requests-2.11.0, scipy-0.18.1, setuptools-32.3.1, simplegeneric-0.8.1, singledispatch-3.4.0.3, six-1.10.0, sympy-1.0, terminado-0.6, tornado-4.4.1, traitlets-4.2.2, widgetsnbextension-1.2.6 Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://bitbucket.org/mpi4py/mpi4py python35-mpi4py]
| align="center" | tools
| align="center" | 2.0.0
| <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 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://python.org/ python35-scipy-stack]
| align="center" | math
| align="center" | 2017a
| <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/ Extensions: arff-2.1.0, backports.shutil_get_terminal_size-1.0.0, bitstring-3.1.5, blist-1.3.6, certifi-2016.8.8, cryptography-1.7.1, Cycler-0.10.0, Cython-0.25.2, dateutil-2.6.0, deap-1.0.2, decorator-4.0.10, ecdsa-0.13, enum34-1.1.6, funcsigs-1.0.2, ipykernel-4.4.1, ipython-5.1.0, ipython_genutils-0.1.0, ipywidgets-5.2.2, Jinja2-2.8, jsonschema-2.5.1, jupyter_client-4.3.0, jupyter_core-4.1.1, lockfile-0.12.2, MarkupSafe-0.23, matplotlib-1.5.3, mistune-0.7.3, mock-2.0.0, mpmath-0.19, nbformat-4.1.0, netaddr-0.7.18, netifaces-0.10.5, nose-1.3.7, notebook-4.2.2, numpy-1.12.0, pandas-0.19.2, paramiko-2.1.1, path.py-10.0, pathlib2-2.1.0, paycheck-1.0.2, pbr-1.10.0, pexpect-4.2.0, pickleshare-0.7.4, prompt_toolkit-1.0.9, ptyprocess-0.5.1, pycrypto-2.6.1, Pygments-2.1.3, pyparsing-2.1.10, pytz-2016.10, PyZMQ-16.0.2, requests-2.11.0, scipy-0.18.1, setuptools-32.3.1, simplegeneric-0.8.1, singledispatch-3.4.0.3, six-1.10.0, sympy-1.0, terminado-0.6, tornado-4.4.1, traitlets-4.2.2, widgetsnbextension-1.2.6 Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://www.qhull.org qhull]
| align="center" | math
| align="center" | 2015.2
| <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 Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://qiime2.org/ qiime2]
| align="center" | -
| align="center" | 2021.11, 2023.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. Homepage: http://qiime2.org/ URL: http://qiime2.org/<br /><br /><br /></div>
|-
| align="center" | [http://qjson.sourceforge.net/ qjson]
| align="center" | tools
| align="center" | 0.9.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa. Homepage: http://qjson.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://sourceforge.net/projects/qrupdate/ qrupdate]
| align="center" | math
| 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/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://www.riverbankcomputing.com/software/qscintilla qscintilla]
| align="center" | tools
| align="center" | 2.10.7
| <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 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://qt.io/ qt]
| 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
| <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/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.synopsys.com/silicon/quantumatk.html quantumatk]
| align="center" | -
| align="center" | 2019.12
| <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>
|-
| align="center" | [https://www.quantum-espresso.org quantumespresso]
| align="center" | chem
| align="center" | 6.0, 6.1, 6.2.2, 6.3, 6.4.1, 6.6
| 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>
|-
| align="center" | [https://www.r-project.org/ r]
| align="center" | tools
| align="center" | 3.3.3, 3.4.0, 3.5.0, 3.5.1, 3.5.2, 3.6.0, 3.6.1, 4.0.0, 4.0.2, 4.1.0, 4.2.1
| Documentation: [[R]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: R is a free software environment for statistical computing and graphics. Homepage: https://www.r-project.org/ URL: https://www.r-project.org/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.r-project.org/ r-bundle-bioconductor]
| align="center" | bio
| align="center" | 3.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/ Extensions: abind-1.4-5, acepack-1.4.1, ade4-1.7-6, affy-1.52.0, affycoretools-1.46.5, affyio-1.44.0, AgiMicroRna-2.24.0, ALDEx2-1.6.0, annaffy-1.46.0, annotate-1.52.1, AnnotationDbi-1.36.2, AnnotationForge-1.16.1, AnnotationHub-2.6.5, ape-4.1, assertthat-0.2.0, assertthat-0.2.0, backports-1.1.0, base64-2.0, base64enc-0.1-3, baySeq-2.8.0, beanplot-1.2, BH-1.62.0-1, BiasedUrn-1.07, bindr-0.1, bindrcpp-0.2, Biobase-2.34.0, BiocGenerics-0.20.0, BiocInstaller-1.24.0, BiocParallel-1.8.2, biomaRt-2.30.0, biomformat-1.2.0, Biostrings-2.42.1, biovizBase-1.22.0, bit-1.1-12, bit64-0.9-7, bitops-1.0-6, blob-1.1.0, BSgenome-1.42.0, BSgenome.Hsapiens.UCSC.hg19-1.4.0, bumphunter-1.14.0, Category-2.40.0, caTools-1.17.1, CGHbase-1.34.0, checkmate-1.8.2, clusterRepro-0.5-1.1, coin-1.2-0, colorspace-1.3-2, corpcor-1.6.9, cummeRbund-2.16.0, curl-2.7, dada2-1.2.2, data.table-1.10.4, DBI-0.7, DEGseq-1.28.0, DEoptimR-1.0-8, derfinder-1.8.5, derfinderHelper-1.8.1, DESeq2-1.14.1, dichromat-2.0-0, digest-0.6.12, digest-0.6.12, diptest-0.75-7, doParallel-1.0.10, doRNG-1.6.6, dplyr-0.7.1, DynDoc-1.52.0, edgeR-3.16.5, ellipse-0.3-8, ensembldb-1.6.2, evaluate-0.10.1, fastcluster-1.1.22, FDb.InfiniumMethylation.hg19-2.2.0, ff-2.2-13, flexmix-2.3-14, foreach-1.4.3, Formula-1.2-1, fpc-2.1-10, futile.logger-1.4.3, futile.logger-1.4.3, futile.logger-1.4.3, futile.options-1.0.0, futile.options-1.0.0, futile.options-1.0.0, gcrma-2.46.0, gdata-2.18.0, gdsfmt-1.10.1, genefilter-1.56.0, geneLenDataBase-1.10.0, geneplotter-1.52.0, GenomeGraphs-1.34.0, GenomeInfoDb-1.10.3, GenomicAlignments-1.10.1, GenomicFeatures-1.26.4, GenomicFiles-1.10.3, GenomicRanges-1.26.4, genoset-1.30.0, GEOquery-2.40.0, GGally-1.3.1, ggbio-1.22.4, ggplot2-2.2.1, glmnet-2.0-10, glue-1.1.1, GO.db-3.4.0, goseq-1.26.0, GOstats-2.40.0, gplots-3.0.1, graph-1.52.0, gridBase-0.4-7, gridExtra-2.2.1, GSEABase-1.36.0, gtable-0.2.0, gtools-3.5.0, Gviz-1.18.2, HCsnip-1.14.0, hgu133plus2.db-3.2.3, highr-0.6, Hmisc-4.0-3, Homo.sapiens-1.3.1, htmlTable-1.9, htmltools-0.3.6, htmlwidgets-0.8, httpuv-1.3.3, httr-1.2.1, hwriter-1.3.2, igraph-1.0.1, illuminaio-0.16.0, impute-1.48.0, interactiveDisplayBase-1.12.0, IRanges-2.8.2, irlba-2.2.1, iterators-1.0.8, jsonlite-1.5, KEGG.db-3.2.3, KEGGgraph-1.32.0, KEGGprofile-1.16.0, KEGGREST-1.14.1, kernlab-0.9-25, knitr-1.16, labeling-0.3, lambda.r-1.1.9, lambda.r-1.1.9, lambda.r-1.1.9, latticeExtra-0.6-28, lazyeval-0.2.0, limma-3.30.13, locfit-1.5-9.1, logspline-2.1.9, lumi-2.26.4, magrittr-1.5, markdown-0.8, marray-1.52.0, maSigPro-1.46.0, matrixStats-0.52.2, mclust-5.3, memoise-1.1.0, metagenomeSeq-1.16.0, methylumi-2.20.0, mime-0.5, minfi-1.20.2, mixOmics-6.1.1, mixOmics-6.1.3, modeltools-0.2-21, multcomp-1.4-6, multtest-2.30.0, munsell-0.4.3, mvtnorm-1.0-6, nleqslv-3.3, NMF-0.20.6, NOISeq-2.18.0, nor1mix-1.2-2, oligoClasses-1.36.0, openssl-0.9.6, org.Hs.eg.db-3.4.0, OrganismDbi-1.16.0, pcaMethods-1.66.0, penalized-0.9-50, perm-1.0-0.0, perm-1.0-0.0, permute-0.9-4, PFAM.db-3.4.0, phyloseq-1.19.1, pkgconfig-2.0.1, pkgmaker-0.22, plogr-0.1-1, plyr-1.8.4, png-0.1-7, polyester-1.10.1, prabclus-2.2-6, preprocessCore-1.36.0, prettyunits-1.0.2, progress-1.1.2, quadprog-1.5-5, qvalue-2.6.0, R.methodsS3-1.7.1, R.oo-1.21.0, R.utils-2.5.0, R6-2.2.2, randomForestSRC-2.4.2, RBGL-1.50.0, RColorBrewer-1.1-2, Rcpp-0.12.11, RcppArmadillo-0.7.900.2.0, RcppParallel-4.3.20, RCurl-1.95-4.5, registry-0.3, ReportingTools-2.14.0, reshape-0.8.6, reshape2-1.4.2, rgl-0.98.1, Rgraphviz-2.18.0, rhdf5-2.18.0, rlang-0.1.1, RNASeqPower-1.14.0, rngtools-1.2.4, robustbase-0.92-7, Rsamtools-1.26.2, RSQLite-2.0, Rsubread-1.24.2, rtracklayer-1.34.2, S4Vectors-0.12.2, samr-2.0, sandwich-2.3-4, scales-0.4.1, shiny-1.0.3, ShortRead-1.32.1, sigaR-1.22.0, siggenes-1.48.0, sm-2.2-5.4, snow-0.4-2, snowfall-1.84-6.1, SNPRelate-1.8.0, sourcetools-0.1.6, SPIA-2.26.0, stringi-1.1.5, stringr-1.2.0, SummarizedExperiment-1.4.0, TeachingDemos-2.10, TH.data-1.0-8, tibble-1.3.3, tidyr-0.6.3, trimcluster-0.1-2, TxDb.Hsapiens.UCSC.hg19.knownGene-3.2.2, VariantAnnotation-1.20.3, vegan-2.4-3, venn-1.2, viridis-0.4.0, viridisLite-0.2.0, XML-3.98-1.9, xtable-1.8-2, xtable-1.8-2, XVector-0.14.1, yaml-2.1.14, zlibbioc-1.20.0, zoo-1.8-0 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/isovic/racon/ racon]
| align="center" | bio
| align="center" | 1.4.13, 20170719
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. Homepage: https://github.com/isovic/racon/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://randomlib.sourceforge.net/html/ randomlib]
| align="center" | -
| align="center" | 1.10
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RandomLib is a C++ interface to the Mersenne Twister random number generator, MT19937 and to the SIMD-oriented Fast Mersenne Twister random number generator, SFMT19937. It provides convenient access to random integers and reals at a variety of precisions. RandomLib also contains new algorithms which permit exact sampling from the normal and discrete normal distributions (provided that the underlying generator is perfect). The emphasis in this implementation is on providing a reliable source of random numbers for scientific applications where there's a premium on accuracy, repeatability, portability, and ease of use. By default, this library uses SFMT's improved method for seeding the generator and it allows access to both the 32-bit and 64-bit versions of MT19937 and SFMT19937 and includes implementations of the SFMT19937 using SSE2 and AltiVec instructions. Homepage: http://randomlib.sourceforge.net/html/ URL: http://randomlib.sourceforge.net/html/<br /><br /><br /></div>
|-
| align="center" | [https://rapidjson.org rapidjson]
| align="center" | -
| align="center" | 1.1.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A fast JSON parser/generator for C++ with both SAX/DOM style API Homepage: https://rapidjson.org URL: https://rapidjson.org<br /><br /><br /></div>
|-
| align="center" | [https://github.com/zorino/ray ray]
| align="center" | bio
| align="center" | 3.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Ray -- Parallel genome assemblies for parallel DNA sequencing. Homepage: https://github.com/zorino/ray Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://re2c.org/ re2c]
| align="center" | -
| align="center" | 1.2.1, 1.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. Homepage: https://re2c.org/ URL: https://re2c.org/<br /><br /><br /></div>
|-
| align="center" | [http://eddylab.org/software/recon/ recon]
| align="center" | bio
| 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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/rlabduke/reduce reduce]
| align="center" | -
| align="center" | 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<br /><br /><br /></div>
|-
| align="center" | [https://github.com/eth-cscs/reframe reframe]
| align="center" | -
| align="center" | 2.21, 3.12.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ReFrame is a framework for writing regression tests for HPC systems. Homepage: https://github.com/eth-cscs/reframe URL: https://github.com/eth-cscs/reframe Compatible modules: python/3.8.10, python/3.9.6, python/3.10.2 Extensions: attrs-21.4.0, certifi-2021.10.8, chardet-4.0.0, idna-3.3, importlib_resources-5.7.1, jsonschema-4.4.0, pyrsistent-0.18.1, reframe-3.12.0, requests-2.27.1, semver-2.13.0, urllib3-1.26.9, zipp-3.8.0<br /><br /><br /></div>
|-
| align="center" | [https://www3.mrc-lmb.cam.ac.uk/relion/ relion]
| align="center" | chem
| align="center" | 3.0
| <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://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" | tools
| align="center" | 1.8.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: REsource MOnitoring for Remote Applications Homepage: https://github.com/TACC/remora Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://repast.github.io/ repasthpc]
| align="center" | bio
| align="center" | 2.2.0
| <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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://bix.ucsd.edu/repeatscout/ repeatscout]
| align="center" | bio
| align="center" | 1.0.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RepeatScout is a tool to discover repetitive substrings in DNA. Homepage: https://bix.ucsd.edu/repeatscout/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/ospray/rkcommon rkcommon]
| align="center" | -
| align="center" | 1.4.2
| <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>
|-
| align="center" | [https://github.com/chedinlab/rlooper.git rlooper]
| align="center" | -
| align="center" | 1.0
| <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/chedinlab/rlooper.git<br /><br /><br /></div>
|-
| align="center" | [http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer rnammer]
| align="center" | bio
| align="center" | 1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RNAmmer 1.2 predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. The method is described in detail in the following article: RNammer: consistent annotation of rRNA genes in genomic sequences. Lagesen K, Hallin PF, Roedland E, Staerfeldt HH, Rognes T Ussery DW. Nucleic Acids Res. Apr 22, 2007. Homepage: http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://root.cern.ch/drupal/ root]
| align="center" | tools
| align="center" | 5.34.36, 6.08.02, 6.14.04
| <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: http://root.cern.ch/drupal/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.rosettacommons.org rosetta]
| align="center" | chem
| align="center" | 3.8
| <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. Homepage: https://www.rosettacommons.org Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://deweylab.github.io/RSEM/ rsem]
| align="center" | bio
| align="center" | 1.3.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RNA-Seq by Expectation-Maximization Homepage: http://deweylab.github.io/RSEM/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.rstudio.com/ rstudio-server]
| align="center" | tools
| align="center" | 1.1.206
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server, bringing the power and productivity of the RStudio IDE to server-based deployments of R. Homepage: https://www.rstudio.com/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.ruby-lang.org ruby]
| align="center" | tools
| align="center" | 2.3.1, 2.6.1, 2.7.1
| <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>
|-
| align="center" | [https://rubygems.org rubygems]
| align="center" | tools
| align="center" | 2.3.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains a collection of popular RubyGems, including ffi, childprocess, json, cabin, backports, arr-pm, clamp, multipart-post, faraday, faraday_middleware, highline, net-http-pipeline, net-http-persistent, multi_json, public_suffix, addressable, gh, launchy, ethon, typhoeus, websocket, pusher-client, diff-lcs, rspec-support, rspec-mocks, rspec-expections, rspec-core, rspec, rack, rack-protection, tilt, sinatra, rack-test, bundler. Homepage: https://rubygems.org Extensions: addressable-2.4.0, arr-pm-0.0.10, backports-3.6.8, bundler-1.15.4, cabin-0.9.0, childprocess-0.5.9, clamp-1.1.1, diff-lcs-1.2.5, ethon-0.10.1, faraday-0.10.0, faraday_middleware-0.10.1, ffi-1.9.14, gh-0.15.0, highline-1.7.8, json-2.0.2, launchy-2.4.3, multi_json-1.12.1, multipart-post-2.0.0, net-http-persistent-2.9.4, net-http-pipeline-1.0.1, public_suffix-2.0.4, pusher-client-0.6.2, rack-1.6.5, rack-protection-1.5.3, rack-test-0.6.3, rspec-3.5.0, rspec-core-3.5.4, rspec-expectations-3.5.0, rspec-mocks-3.5.0, rspec-support-3.5.0, sinatra-1.4.7, tilt-2.0.5, typhoeus-0.6.9, websocket-1.2.3 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.rust-lang.org rust]
| 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
| <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>
|-
| align="center" | [https://github.com/najoshi/sabre sabre]
| align="center" | bio
| align="center" | 1.00
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A barcode demultiplexing and trimming tool for FastQ files Homepage: https://github.com/najoshi/sabre Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/COMBINE-lab/salmon salmon]
| align="center" | bio
| align="center" | 0.9.1
| <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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/COMBINE-lab/salmon/ salmonbeta]
| align="center" | bio
| align="center" | 0.6.0
| <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. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment. Homepage: https://github.com/COMBINE-lab/salmon/ URL: https://github.com/COMBINE-lab/salmon/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://lomereiter.github.io/sambamba/ sambamba]
| align="center" | bio
| align="center" | 0.6.7, 0.7.1, 0.8.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. Homepage: https://lomereiter.github.io/sambamba/ URL: https://lomereiter.github.io/sambamba/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/GregoryFaust/samblaster samblaster]
| align="center" | bio
| align="center" | 0.1.24
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: samblaster: a tool to mark duplicates and extract discordant and split reads from sam files Homepage: https://github.com/GregoryFaust/samblaster Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://samstat.sourceforge.net/ samstat]
| align="center" | -
| align="center" | 1.5.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Displaying sequence statistics for next generation sequencing Homepage: http://samstat.sourceforge.net/ URL: http://samstat.sourceforge.net/<br /><br /><br /></div>
|-
| align="center" | [https://www.htslib.org/ samtools]
| align="center" | bio
| align="center" | 0.1.20, 1.3.1, 1.5, 1.9, 1.10
| <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>
|-
| align="center" | [http://www.scala-sbt.org/ sbt]
| align="center" | tools
| align="center" | 1.1.1, 1.3.13
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: sbt is a build tool for Scala, Java, and more. It requires Java 1.8 or later. sbt uses a small number of concepts to support flexible and powerful build definitions. There are not that many concepts, but sbt is not exactly like other build systems and there are details you will stumble on if you haven t read the documentation. The Getting Started Guide covers the concepts you need to know to create and maintain an sbt build definition. It is highly recommended to read the Getting Started Guide. Homepage: http://www.scala-sbt.org/ URL: http://www.scala-sbt.org/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.netlib.org/scalapack/ scalapack]
| align="center" | math
| align="center" | 2.0.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. Homepage: http://www.netlib.org/scalapack/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://python.org/ scipy-stack]
| align="center" | math
| 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/3.9, 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>
|-
| align="center" | [https://gforge.inria.fr/projects/scotch/ scotch]
| align="center" | math
| align="center" | 6.0.4, 6.0.6, 6.0.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. Homepage: https://gforge.inria.fr/projects/scotch/ URL: https://gforge.inria.fr/projects/scotch/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://github.com/ucdavis-bioinformatics/scythe scythe]
| align="center" | -
| align="center" | 0.994
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. Homepage: https://github.com/ucdavis-bioinformatics/scythe URL: https://github.com/ucdavis-bioinformatics/scythe<br /><br /><br /></div>
|-
| align="center" | [https://www.disneyanimation.com/technology/seexpr.html seexpr]
| align="center" | vis
| align="center" | 2.11
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SeExpr is a simple expression language that we use to provide artistic control and customization to our core software. We use it for procedural geometry synthesis, image synthesis, simulation control, and much more. Homepage: https://www.disneyanimation.com/technology/seexpr.html Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://www.bioinf.uni-leipzig.de/Software/segemehl/ segemehl]
| align="center" | -
| align="center" | 0.3.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/<br /><br /><br /></div>
|-
| align="center" | [https://www.seqan.de/ seqan-library]
| align="center" | -
| align="center" | 1.4.2, 2.4.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data Homepage: https://www.seqan.de/ URL: https://www.seqan.de/<br /><br /><br /></div>
|-
| align="center" | [https://bioinf.shenwei.me/seqkit/ seqkit]
| align="center" | -
| align="center" | 0.13.2, 0.15.0, 2.3.1
| <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>
|-
| align="center" | [https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html shapeit]
| align="center" | -
| align="center" | 2.r904
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. Homepage: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html URL: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html<br /><br /><br /></div>
|-
| align="center" | [http://www.shengbte.org/ shengbte]
| align="center" | phys
| align="center" | 1.1.1
| <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/ Extensions: thirdorder-1.0.2 Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [https://github.com/sharpton/shotmap shotmap]
| align="center" | bio
| align="center" | 1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Shotmap is a software workflow that functionally annotates and compares shotgun metagenomes. Specifically, it will: 1. Compared unassembled or assembled metagenomic sequences to a protein family database 2. Calculate metagenome functional abundance and diversity 3. Compare metagenomes using a variety of statistical and ecological tools 4. Identify protein families that differentiate metagenomes using robust statistical tests Shotmap can be run on a multicore computer or can optionally interface with an SGE-configured computing cluste (i.e., a cloud). Shotmap can also optionally manage the information and data associated with this workflow in a relational database. Homepage: https://github.com/sharpton/shotmap Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/jonathonl/shrinkwrap shrinkwrap]
| align="center" | -
| align="center" | 1.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A std::streambuf wrapper for compression formats. Homepage: https://github.com/jonathonl/shrinkwrap URL: https://github.com/jonathonl/shrinkwrap<br /><br /><br /></div>
|-
| align="center" | [http://departments.icmab.es/leem/siesta siesta]
| align="center" | chem
| align="center" | 4.0, 4.1-b3
| <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 Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp signalp]
| align="center" | bio
| align="center" | 4.1f
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. Homepage: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp URL: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.singular.uni-kl.de/ singular]
| align="center" | -
| align="center" | 4.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. Homepage: https://www.singular.uni-kl.de/ URL: https://www.singular.uni-kl.de/<br /><br /><br /></div>
|-
| align="center" | [http://www.riverbankcomputing.com/software/sip/ sip]
| align="center" | tools
| align="center" | 4.19.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. Homepage: http://www.riverbankcomputing.com/software/sip/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.slicer.org/ slicer]
| align="center" | -
| align="center" | 4.10.1, 4.11.20210226
| <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>
|-
| align="center" | [http://korflab.ucdavis.edu/software.html snap]
| align="center" | bio
| align="center" | 2013-11-29
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SNAP: Semi-HMM-based Nucleic Acid Parser gene prediction tool - Version Releaseed on: 11/29/2013. Homepage: http://korflab.ucdavis.edu/software.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/google/snappy snappy]
| align="center" | tools
| align="center" | 1.1.3, 1.1.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. Homepage: https://github.com/google/snappy URL: https://github.com/google/snappy Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://pcingola.github.io/SnpEff/ snpeff]
| align="center" | bio
| align="center" | 4.3t, 5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). Homepage: https://pcingola.github.io/SnpEff/ URL: https://pcingola.github.io/SnpEff/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://soap.genomics.org.cn/index.html soapdenovo2]
| align="center" | bio
| align="center" | r240
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. Homepage: http://soap.genomics.org.cn/index.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://bioinfo.lifl.fr/RNA/sortmerna/ sortmerna]
| align="center" | bio
| align="center" | 2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. Homepage: http://bioinfo.lifl.fr/RNA/sortmerna/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://cab.spbu.ru/software/spades/ spades]
| align="center" | bio
| align="center" | 3.10.1, 3.13.0, 3.13.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/ URL: http://cab.spbu.ru/software/spades/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://spark.apache.org spark]
| align="center" | tools
| align="center" | 2.1.0, 2.1.1, 2.2.0, 2.2.1, 2.3.0, 2.4.4, 3.0.0, 3.3.0
| Documentation: [[Apache Spark]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Spark is Hadoop MapReduce done in memory Homepage: http://spark.apache.org URL: http://spark.apache.org Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://spectralib.org/index.html spectra]
| align="center" | -
| align="center" | 0.9.0
| <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>
|-
| align="center" | [https://github.com/hall-lab/speedseq speedseq]
| align="center" | bio
| align="center" | 0.1.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A flexible framework for rapid genome analysis and interpretation Homepage: https://github.com/hall-lab/speedseq URL: https://github.com/hall-lab/speedseq Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/atztogo/spglib spglib]
| align="center" | chem
| align="center" | 1.9.9
| <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 Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://www.sqlite.org/ sqlite]
| align="center" | -
| align="center" | 3.43.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SQLite: SQL Database Engine in a C Library Homepage: https://www.sqlite.org/ URL: https://www.sqlite.org/<br /><br /><br /></div>
|-
| align="center" | [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std sra-toolkit]
| align="center" | bio
| align="center" | 2.8.2-1, 2.9.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread sspace-longread]
| align="center" | bio
| align="center" | 1-1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SSPACE-LongRead is a stand-alone program for scaffolding pre-assembled contigs using long reads (e.g. PacBio RS reads). Homepage: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE-longread Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://github.com/nsoranzo/sspace_basic sspace_basic]
| align="center" | bio
| align="center" | 2.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension Homepage: https://github.com/nsoranzo/sspace_basic Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://catchenlab.life.illinois.edu/stacks/ stacks]
| align="center" | bio
| align="center" | 1.45, 1.46
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Homepage: http://catchenlab.life.illinois.edu/stacks/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm]
| align="center" | phys
| align="center" | 11.06.011-R8, 12.04.011-R8, 12.06.011-R8, 13.04.010-R8, 13.06.012-R8, 14.02.012-R8, 14.04.013-R8, 14.06.013-R8, 15.04.010-R8, 16.02.008-R8, 16.02.009-R8, 16.04.007-R8, 16.04.012-R8, 16.06.008-R8, 17.02.007-R8, 17.02.008-R8, 17.04.007-R8, 17.04.008-R8, 17.06.007-R8, 17.06.008-R8, 18.02.008-R8, 18.04.008-R8, 18.06.006-R8
| Documentation: [[StarCCM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses double precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://mdx.plm.automation.siemens.com/star-ccm-plus starccm-mixed]
| align="center" | phys
| align="center" | 11.06.011, 12.04.011, 12.06.011, 13.04.010, 13.06.012, 14.02.012, 14.04.013, 14.06.013, 15.04.010, 16.02.008, 16.02.009, 16.04.007, 16.04.012, 16.06.008, 17.02.007, 17.02.008, 17.04.007, 17.04.008, 17.06.007, 17.06.008, 18.02.008, 18.04.008, 18.06.006
| Documentation: [[StarCCM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Predicting the real-world performance of a product requires simulation tools that span a variety of engineering disciplines. STAR-CCM+ is an all-in-one solution that delivers accurate and efficient multidisciplinary technologies in a single integrated user interface. This version uses mixed precision. Homepage: http://mdx.plm.automation.siemens.com/star-ccm-plus URL: http://mdx.plm.automation.siemens.com/star-ccm-plus Keyword:phys<br /><br /><br /></div>
|-
| align="center" | [http://ccb.jhu.edu/software/stringtie/ stringtie]
| align="center" | bio
| align="center" | 1.3.4d
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Homepage: http://ccb.jhu.edu/software/stringtie/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://su2.stanford.edu su2]
| align="center" | math
| align="center" | 5.0.0, 6.0.1, 6.2.0, 7.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open-source collection of software tools written in C++ for performing Partial Differential Equation (PDE) analysis and solving PDE-constrained optimization problems. The toolset is designed with computational fluid dynamics and aerodynamic shape optimization in mind. Homepage: http://su2.stanford.edu URL: http://su2.stanford.edu Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://subread.sourceforge.net/ subread]
| align="center" | bio
| align="center" | 1.5.2
| <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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://faculty.cse.tamu.edu/davis/suitesparse.html suitesparse]
| align="center" | math
| align="center" | 4.5.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuiteSparse is a collection of libraries manipulate sparse matrices. - Homepage: http://faculty.cse.tamu.edu/davis/suitesparse.html Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://metabarcoding.org/sumatra sumaclust]
| align="center" | bio
| align="center" | 1.0.20
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Homepage: http://metabarcoding.org/sumatra Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ superlu]
| align="center" | math
| align="center" | 5.1.1, 5.2.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Homepage: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome supernova]
| align="center" | bio
| align="center" | 2.0.0, 2.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Supernova is delivered as a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its own required software dependencies, which are pre-compiled to run on a range of Linux distributions. Homepage: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome URL: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://www.swi-prolog.org/ swi-prolog]
| align="center" | -
| align="center" | 9.0.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SWI-Prolog offers a comprehensive free Prolog environment. Homepage: https://www.swi-prolog.org/ URL: https://www.swi-prolog.org/<br /><br /><br /></div>
|-
| align="center" | [http://www.swig.org/ swig]
| align="center" | -
| align="center" | 3.0.12, 4.0.1
| <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/<br /><br /><br /></div>
|-
| align="center" | [http://samtools.sourceforge.net tabix]
| align="center" | bio
| align="center" | 0.2.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Generic indexer for TAB-delimited genome position files Homepage: http://samtools.sourceforge.net Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://bioinf.shenwei.me/taxonkit/ taxonkit]
| align="center" | -
| align="center" | 0.6.2
| <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" | [https://github.com/oneapi-src/oneTBB tbb]
| align="center" | tools
| align="center" | 2018_U5, 2017.2.132, 2020.2
| <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" | -
| align="center" | 25.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank Homepage: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ URL: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/<br /><br /><br /></div>
|-
| align="center" | [http://www.tcl.tk/ tcl]
| align="center" | tools
| align="center" | 8.5.19, 8.6.8
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Homepage: http://www.tcl.tk/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://developer.nvidia.com/tensorrt tensorrt]
| align="center" | -
| 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>
|-
| align="center" | [http://wiki.tcl.tk/1877 tktable]
| align="center" | tools
| 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 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm]
| align="center" | bio
| 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 Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://ccb.jhu.edu/software/tophat/ tophat]
| align="center" | bio
| align="center" | 2.1.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TopHat is a fast splice junction mapper for RNA-Seq reads. Homepage: http://ccb.jhu.edu/software/tophat/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://torch.ch/ torch]
| align="center" | ai
| align="center" | 20170530, 20170731
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. Homepage: http://torch.ch/ Keyword:ai<br /><br /><br /></div>
|-
| align="center" | [http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/ trans-abyss]
| align="center" | bio
| align="center" | 1.5.5
| <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" | bio
| align="center" | 3.0.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. - Homepage: https://transdecoder.github.io/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://hibberdlab.com/transrate/ transrate]
| align="center" | bio
| 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>
|-
| align="center" | [http://bitbucket.org/nygcresearch/treemix treemix]
| align="center" | -
| align="center" | 1.13
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. Homepage: http://bitbucket.org/nygcresearch/treemix URL: http://bitbucket.org/nygcresearch/treemix<br /><br /><br /></div>
|-
| align="center" | [https://tandem.bu.edu/trf/trf.html trf]
| align="center" | bio
| align="center" | 4.09
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Tandem repeats finder: a program to analyze DNA sequences. Legacy version. Homepage: https://tandem.bu.edu/trf/trf.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://trilinos.sandia.gov/ trilinos]
| align="center" | tools
| align="center" | 12.10.1
| <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: http://trilinos.sandia.gov/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://trimal.cgenomics.org/ trimal]
| align="center" | bio
| 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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.usadellab.org/cms/?page=trimmomatic trimmomatic]
| align="center" | bio
| align="center" | 0.36, 0.39
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. Homepage: http://www.usadellab.org/cms/?page=trimmomatic URL: http://www.usadellab.org/cms/?page=trimmomatic Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://trinityrnaseq.github.io/ trinity]
| align="center" | bio
| align="center" | 2.4.0, 2.5.0, 2.8.4
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Homepage: http://trinityrnaseq.github.io/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://trinotate.github.io/ trinotate]
| align="center" | bio
| align="center" | 3.0.2
| <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/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://lowelab.ucsc.edu/ trnascan-se]
| align="center" | bio
| align="center" | 2.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: tRNAscan-SE: An improved tool for transfer RNA detection, Patricia Chan and Todd Lowe, School of Engineering, University of California, Santa Cruz, CA. tRNAscan-SE was written in the PERL (version 5.0) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. Homepage: http://lowelab.ucsc.edu/ URL: http://lowelab.ucsc.edu/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://www.openucx.org/ ucx]
| align="center" | -
| align="center" | 1.5.2, 1.8.0
| <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: http://www.openucx.org/ URL: http://www.openucx.org/<br /><br /><br /></div>
|-
| align="center" | [https://www.unidata.ucar.edu/software/udunits/ udunits]
| align="center" | tools
| align="center" | 2.2.24, 2.2.26
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. Homepage: https://www.unidata.ucar.edu/software/udunits/ URL: https://www.unidata.ucar.edu/software/udunits/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://www.unixodbc.org unixodbc]
| align="center" | -
| align="center" | 2.3.7, 2.3.9
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: unixODBC provides a uniform interface between application and database driver Homepage: https://www.unixodbc.org URL: https://www.unixodbc.org<br /><br /><br /></div>
|-
| align="center" | [http://valgrind.org/downloads/ valgrind-mpi]
| align="center" | tools
| align="center" | 3.13.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Valgrind: Debugging and profiling tools Homepage: http://valgrind.org/downloads/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://github.com/dkoboldt/varscan varscan]
| align="center" | -
| align="center" | 2.4.1, 2.4.2
| <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" | [https://github.com/henniggroup/VASPsol) vasp]
| align="center" | chem
| align="center" | 5.4.4
| Documentation: [[VASP]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, based on Density Futional Theory (DFT). In this version VASPsol (https://github.com/henniggroup/VASPsol) has been implemented to the original version of vasp Homepage: http://www.vasp.at Keyword:chem<br /><br /><br /></div>
|-
| align="center" | [https://www.vaultproject.io/ vault]
| align="center" | -
| align="center" | 1.0.3
| <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://vcftools.github.io vcftools]
| align="center" | bio
| align="center" | 0.1.14
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. - Homepage: https://vcftools.github.io Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://csg.sph.umich.edu/kang/verifyBamID/index.html verifybamid]
| align="center" | bio
| align="center" | 1.1.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps. Homepage: http://csg.sph.umich.edu/kang/verifyBamID/index.html Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [http://viennacl.sourceforge.net/ viennacl]
| align="center" | math
| align="center" | 1.7.1
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ViennaCL is a free open-source linear algebra library for computations on many-core architectures (GPUs, MIC) and multi-core CPUs. The library is written in C++ and supports CUDA, OpenCL, and OpenMP (including switches at runtime). Homepage: http://viennacl.sourceforge.net/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [http://www.tbi.univie.ac.at/RNA/ viennarna]
| align="center" | bio
| align="center" | 2.4.9, 2.4.10, 2.4.11
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. Homepage: http://www.tbi.univie.ac.at/RNA/ Keyword:bio<br /><br /><br /></div>
|-
| align="center" | [https://wci.llnl.gov/simulation/computer-codes/visit visit]
| align="center" | vis
| align="center" | 2.13.3
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Homepage: https://wci.llnl.gov/simulation/computer-codes/visit URL: https://wci.llnl.gov/simulation/computer-codes/visit Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://www.ks.uiuc.edu/Research/vmd vmd]
| align="center" | vis
| align="center" | 1.9.3
| <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: http://www.ks.uiuc.edu/Research/vmd Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://math.lbl.gov/voro++/ voro++]
| align="center" | math
| 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++/ Keyword:math<br /><br /><br /></div>
|-
| align="center" | [https://github.com/torognes/vsearch vsearch]
| align="center" | bio
| align="center" | 2.4.3
| <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>
|-
| align="center" | [http://www.vtk.org vtk]
| align="center" | vis
| align="center" | 6.3.0, 8.0.0
| <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 Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [https://software.intel.com/en-us/vtune vtune]
| align="center" | tools
| 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 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://code.ornl.gov/neams-workbench/wasp wasp]
| align="center" | -
| align="center" | 3.1.4, 4.0.3
| <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>
|-
| align="center" | [https://www.geometrictools.com/ wildmagic]
| align="center" | -
| align="center" | 5.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Geometric Tools Wild Magic is a C++ library for real-time computer graphics and physics, mathematics, geometry, numerical analysis, and image analysis. Homepage: https://www.geometrictools.com/ URL: https://www.geometrictools.com/<br /><br /><br /></div>
|-
| align="center" | [http://www.wrf-model.org wps]
| align="center" | geo
| align="center" | 3.8.0, 3.8.1
| <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 Homepage: http://www.wrf-model.org Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [http://www.wrf-model.org wrf]
| align="center" | geo
| align="center" | 3.8.0, 3.8.1
| <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>
|-
| align="center" | [http://www.openwfm.org/wiki/WRF-SFIRE wrf-fire]
| align="center" | geo
| align="center" | 20170625
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and terrain slope. The fire spread is implemented by the level set method. Homepage: http://www.openwfm.org/wiki/WRF-SFIRE Keyword:geo<br /><br /><br /></div>
|-
| align="center" | [http://www.xcrysden.org/ xcrysden]
| align="center" | vis
| align="center" | 1.5.60
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. Homepage: http://www.xcrysden.org/ URL: http://www.xcrysden.org/ Keyword:vis<br /><br /><br /></div>
|-
| align="center" | [http://xerces.apache.org/xerces-c/ xerces-c++]
| align="center" | tools
| align="center" | 3.1.1, 3.2.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. Homepage: http://xerces.apache.org/xerces-c/ URL: http://xerces.apache.org/xerces-c/ Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod xml-libxml]
| align="center" | -
| align="center" | 2.0205
| <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>
|-
| align="center" | [https://launchpad.net/xmlf90/ xmlf90]
| align="center" | tools
| align="center" | 1.5.4
| <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>
|-
| align="center" | [https://github.com/xtensor-stack/xtensor xtensor]
| align="center" | -
| align="center" | 0.24.2
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions. Homepage: https://github.com/xtensor-stack/xtensor URL: https://github.com/xtensor-stack/xtensor<br /><br /><br /></div>
|-
| align="center" | [https://www.dkrz.de/redmine/projects/yaxt yaxt]
| align="center" | tools
| align="center" | 0.5.1
| <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 Keyword:tools<br /><br /><br /></div>
|-
| align="center" | [http://www.zeromq.org/ zeromq]
| align="center" | tools
| align="center" | 4.2.5
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. Homepage: http://www.zeromq.org/ Keyword:tools<br /><br /><br /></div>
|}<noinclude>{{NOINDEX}}</noinclude>

Revision as of 15:56, 28 June 2024

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