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| align="center" | phys | | 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 | | 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: [[ | | 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> | ||
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| align="center" | [http://www.ansys.com ansysedt] | | align="center" | [http://www.ansys.com ansysedt] | ||
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| align="center" | [https://apptainer.org apptainer] | | align="center" | [https://apptainer.org apptainer] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 1.1.3, 1.1.5, 1.1.6, 1.1.8 | | 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> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apptainer/Singularity is an application containerization solution for High-Performance Computing (HPC). The goal of Apptainer is to allow for "mobility of computing": an application containerized on one Linux system should be able to run on another system, as it is, and without the need to reconcile software dependencies and Linux version differences between the source and target systems. Homepage: https://apptainer.org URL: https://apptainer.org<br /><br /><br /></div> | ||
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| align="center" | math | | align="center" | math | ||
| align="center" | 3.4.0, 3.5.0 | | 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. | | <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> | ||
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| align="center" | [http://downloads.asperasoft.com/ ascp] | | align="center" | [http://downloads.asperasoft.com/ ascp] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 3.5.4 | | align="center" | 3.5.4 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Aspera ASCP is a high speed file transfer software Homepage | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Aspera ASCP is a high speed file transfer software Homepage: http://downloads.asperasoft.com/ Keyword:tools<br /><br /><br /></div> | ||
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| align="center" | [http://bioinf.uni-greifswald.de/augustus/ augustus] | | align="center" | [http://bioinf.uni-greifswald.de/augustus/ augustus] | ||
| Line 118: | Line 118: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.4.1 | | 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 | | <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> | ||
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| align="center" | [http://genome.sph.umich.edu/wiki/BamUtil bamutil] | | align="center" | [http://genome.sph.umich.edu/wiki/BamUtil bamutil] | ||
| Line 138: | Line 138: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.4, 1.5, 1.9 | | 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 | | <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> | ||
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| align="center" | [https://faculty.washington.edu/browning/beagle/beagle.html beagle] | | align="center" | [https://faculty.washington.edu/browning/beagle/beagle.html beagle] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. - Homepage: https://github.com/beagle-dev/beagle-lib Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. - Homepage: https://github.com/beagle-dev/beagle-lib Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [http:// | | align="center" | [http://beast2.org/ beast] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.8.2, 2.4.0 | | 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:// | | <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> | ||
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| align="center" | [http://bedops.readthedocs.io/en/latest/index.html bedops] | | align="center" | [http://bedops.readthedocs.io/en/latest/index.html bedops] | ||
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| <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> | | <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> | ||
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| align="center" | [ | | align="center" | [https://bioperl.org/ bioperl] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.7.1, 1.7.5, 1.7.7, 1.7.8 | | align="center" | 1.7.1, 1.7.5, 1.7.7, 1.7.8 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Homepage: | | <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> | ||
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| align="center" | [https://www.gnu.org/software/bison bison] | | align="center" | [https://www.gnu.org/software/bison bison] | ||
| Line 203: | Line 203: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 3.5 | | 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. | | <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> | ||
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| align="center" | [https://www.blender.org/ blender] | | align="center" | [https://www.blender.org/ blender] | ||
| Line 243: | Line 243: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.3.0, 2.3.3.1, 2.3.5 | | 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. | | <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> | ||
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| align="center" | [https://github.com/BUStools/bustools bustools] | | align="center" | [https://github.com/BUStools/bustools bustools] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 20151002 | | align="center" | 20151002 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: CAP3 assembly program Homepage | | <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> | ||
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| align="center" | [https://github.com/catchorg/Catch2 catch2] | | align="center" | [https://github.com/catchorg/Catch2 catch2] | ||
| Line 283: | Line 283: | ||
| align="center" | geo | | align="center" | geo | ||
| align="center" | 4_0_a02 | | align="center" | 4_0_a02 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Climate System Model (CCSM) is a coupled climate model for simulating the earth's climate system. Composed of four separate models simultaneously simulating the earth's atmosphere, ocean, land surface and sea-ice, and one central coupler component, the CCSM allows researchers to conduct fundamental research into the earth's past, present and future climate states. Homepage | | <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> | ||
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| align="center" | [https://code.zmaw.de/projects/cdo cdo] | | align="center" | [https://code.zmaw.de/projects/cdo cdo] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.1.0 | | align="center" | 2.1.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Cell Ranger is a set of analysis pipelines that process Chromium single cell 3-RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 and later support libraries generated by the Chromium Single Cell 3i-v1 and v2 reagent kits, whereas Cell Ranger 1.1 and earlier do not support v2 libraries. Cell Ranger includes four main gene expression pipelines: - cellranger mkfastq wraps Illumina's bcl2fastq to correctly demultiplex Chromium-prepared sequencing samples and to convert barcode and read data to FASTQ files. - cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, and UMI counting. - cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the gene-barcode matrices and analysis on the combined data. - cellranger reanalyze takes gene-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using tunable parameter settings. These pipelines combine Chromium-specific algorithms with the widely used RNA-seq aligner STAR. Output is delivered in standard BAM, MEX, CSV, HDF5 and HTML formats that are augmented with cellular information. Homepage | | <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> | ||
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| align="center" | [https://github.com/infphilo/centrifuge centrifuge] | | align="center" | [https://github.com/infphilo/centrifuge centrifuge] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. Homepage: http://uscilab.github.io/cereal/ URL: http://uscilab.github.io/cereal/<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. Homepage: http://uscilab.github.io/cereal/ URL: http://uscilab.github.io/cereal/<br /><br /><br /></div> | ||
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| align="center" | [http://www.cesm.ucar.edu/models/ | | align="center" | [http://www.cesm.ucar.edu/models/cesm2/ cesm] | ||
| align="center" | geo | | align="center" | geo | ||
| align="center" | 1_2_2, 2.1.1, 2.1.3 | | align="center" | 1_2_2, 2.1.1, 2.1.3 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. Homepage: http://www.cesm.ucar.edu/models/ | | <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> | ||
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| align="center" | [https://heasarc.gsfc.nasa.gov/docs/software/fitsio// cfitsio] | | align="center" | [https://heasarc.gsfc.nasa.gov/docs/software/fitsio// cfitsio] | ||
| Line 323: | Line 323: | ||
| align="center" | phys | | align="center" | phys | ||
| align="center" | 3.3.1 | | 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 | | <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> | ||
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| align="center" | [http://chapel.cray.com chapel-single] | | align="center" | [http://chapel.cray.com chapel-single] | ||
| Line 348: | Line 348: | ||
| align="center" | math | | align="center" | math | ||
| align="center" | 2.3.1.1, 2.4.1.0, 2.4.1.2 | | 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 | | <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> | ||
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| align="center" | [https://www.cmake.org cmake] | | align="center" | [https://www.cmake.org cmake] | ||
| Line 422: | Line 422: | ||
| align="center" | [https://developer.nvidia.com/cudnn cudnn] | | align="center" | [https://developer.nvidia.com/cudnn cudnn] | ||
| align="center" | math | | align="center" | math | ||
| align="center" | 5.1, 6 | | align="center" | 5.1, 6.0, 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> | | <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> | ||
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| align="center" | tools | | align="center" | tools | ||
| align="center" | 1.1.8, 2.0.7 | | align="center" | 1.1.8, 2.0.7 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: .NET is a free, cross-platform, open source developer platform for building many different types of applications | | <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> | ||
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| align="center" | [https://github.com/google/double-conversion double-conversion] | | align="center" | [https://github.com/google/double-conversion double-conversion] | ||
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| <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> | | <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> | ||
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| align="center" | [ | | align="center" | [https://libexpat.github.io expat] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2.2.5, 2.2.6, 2.2.9, 2.2.10 | | 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: | | <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" | [https://bitbucket.org/jerlar73/fast-gbs fast-gbs] | ||
| Line 608: | Line 608: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.1.10 | | align="center" | 2.1.10 | ||
| <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> | | 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" | [http://hannonlab.cshl.edu/fastx_toolkit/ fastx-toolkit] | ||
| Line 633: | Line 633: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 0.2.0 | | align="center" | 0.2.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage | | <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" | [https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release flexiblas] | ||
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| align="center" | phys | | align="center" | phys | ||
| align="center" | 16.1 | | align="center" | 16.1 | ||
| Documentation: [[ | | 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" | [https://fmriprep.org/ fmriprep] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Extract sequences from a fastx file given a subsequence or identifier Homepage: https://github.com/ctSkennerton/fxtract<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Extract sequences from a fastx file given a subsequence or identifier Homepage: https://github.com/ctSkennerton/fxtract<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [ | | align="center" | [http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2clib] | ||
| align="center" | geo | | align="center" | geo | ||
| align="center" | 1.6.0 | | 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: | | <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" | [http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ g2lib] | ||
| Line 743: | Line 743: | ||
| align="center" | phys | | align="center" | phys | ||
| align="center" | 10.02.p03, 10.04.p02, 10.05.p01 | | 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 | | <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" | [https://geant4.cern.ch/ geant4-data] | ||
| Line 827: | Line 827: | ||
| align="center" | [https://www.golang.org go] | | align="center" | [https://www.golang.org go] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 1.10.3, 1.14.1, 1.14.4, 1.18.3 | | 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> | | <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> | ||
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| Line 938: | Line 938: | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2.2 | | 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. | | <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" | [http://www.htslib.org/ htslib] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.4, 1.5, 1.9 | | 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 | | <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" | [https://www.open-mpi.org/projects/hwloc/ hwloc] | ||
| Line 980: | Line 980: | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes Homepage: https://software.intel.com/en-us/articles/intel-mpi-benchmarks URL: https://software.intel.com/en-us/articles/intel-mpi-benchmarks<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes Homepage: https://software.intel.com/en-us/articles/intel-mpi-benchmarks URL: https://software.intel.com/en-us/articles/intel-mpi-benchmarks<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [ | | align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html imkl] | ||
| align="center" | math | | align="center" | math | ||
| align="center" | 11.1.4.214, 11.3.4.258, 2017.1.132, 2017.4.239, 2018.1.163, 2018.3.222, 2019.2.187, 2019.3.199, 2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0 | | align="center" | 11.1.4.214, 11.3.4.258, 2017.1.132, 2017.4.239, 2018.1.163, 2018.3.222, 2019.2.187, 2019.3.199, 2020.1.217, 2021.2.0, 2021.4.0, 2022.1.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Math Kernel Library | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel oneAPI Math Kernel Library Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html Keyword:math<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [http://software.intel.com/en-us/intel-mpi-library/ impi] | | align="center" | [http://software.intel.com/en-us/intel-mpi-library/ impi] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.3.2 | | align="center" | 2.3.2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 Homepage | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 - Homepage: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html Keyword:bio<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://jmarchini.org/software/#impute-5 impute5] | | align="center" | [https://jmarchini.org/software/#impute-5 impute5] | ||
| Line 1,010: | Line 1,010: | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications Homepage: http://software.intel.com/en-us/intel-inspector-xe Keyword:tools<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications Homepage: http://software.intel.com/en-us/intel-inspector-xe Keyword:tools<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [ | | align="center" | [https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html intel] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2014.6, 2016.4, 2017.1, 2017.5, 2018.3, 2019.3, 2020.1.217, 2021.2.0, 2022.1.0 | | align="center" | 2014.6, 2016.4, 2017.1, 2017.5, 2018.3, 2019.3, 2020.1.217, 2021.2.0, 2022.1.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel C, C++ and Fortran compilers (classic and oneAPI) Homepage: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html URL: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html Keyword:tools<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html intel-opencl] | | align="center" | [https://software.intel.com/content/www/us/en/develop/articles/intel-cpu-runtime-for-opencl-applications-with-sycl-support.html intel-opencl] | ||
| Line 1,023: | Line 1,023: | ||
| align="center" | mpi | | align="center" | mpi | ||
| align="center" | 2018.3.222, 2019.3.199 | | 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 | | <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" | [https://intelxed.github.io/ intelxed] | ||
| Line 1,048: | Line 1,048: | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 2020a, 2020b, 2021a, 2022a, 2023a, 2023b | | align="center" | 2020a, 2020b, 2021a, 2022a, 2023a, 2023b | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains ipykernel | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains ipykernel 2023b and its dependencies Homepage: https://ipython.org/ URL: https://ipython.org/ Compatible modules: python/3.9, python/3.10, python/3.11 Extensions: asttokens-2.2.1, backcall-0.2.0, comm-0.1.4, debugpy-1.6.7.post1, decorator-5.1.1, executing-1.2.0, importlib_metadata-6.8.0, ipykernel-6.25.1, ipython-8.15.0, ipython_genutils-0.2.0, jedi-0.19.0, jupyter_client-8.3.1, jupyter_core-5.3.1, matplotlib_inline-0.1.6, nest_asyncio-1.5.7, packaging-23.1, parso-0.8.3, pexpect-4.8.0, pickleshare-0.7.5, platformdirs-2.6.2, prompt_toolkit-3.0.39, psutil-5.9.5, ptyprocess-0.7.0, pure_eval-0.2.2, Pygments-2.16.1, python-dateutil-2.8.2, pyzmq-25.1.1, six-1.16.0, stack_data-0.6.2, tornado-6.3.3, traitlets-5.9.0, wcwidth-0.2.6, zipp-3.16.2<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://ipython.org/ ipython-kernel] | | align="center" | [https://ipython.org/ ipython-kernel] | ||
| Line 1,080: | Line 1,080: | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. Homepage: https://www.ece.uvic.ca/~frodo/jasper/ URL: https://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. Homepage: https://www.ece.uvic.ca/~frodo/jasper/ URL: https://www.ece.uvic.ca/~frodo/jasper/ Keyword:vis<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [ | | align="center" | [http://openjdk.java.net java] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 1.7.0_80, 1.8.0_121, 1.8.0_192, 11.0. | | 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: | | 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" | [http://www.genome.umd.edu/jellyfish.html jellyfish] | ||
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| align="center" | chem | | align="center" | chem | ||
| align="center" | 20170331 | | 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: | | 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" | [http://lammps.sandia.gov/ lammps-omp] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 20170331, 20170811 | | 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: | | 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" | [http://lammps.sandia.gov/ lammps-user-intel] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 20170331, 20170811 | | 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: | | 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" | [http://last.cbrc.jp/ last] | ||
| Line 1,235: | Line 1,235: | ||
| <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> | | <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" | [ | | align="center" | [https://www.tddft.org/programs/libxc libxc] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 3.0.0, 4.2.1, 4.2.3, 4.3.4 | | 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: | | <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" | [https://github.com/hfp/libxsmm libxsmm] | ||
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| <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> | | <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" | [ | | align="center" | [http://www.mathworks.com/products/matlab matlab] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2014a, 2016b, 2017a, 2018a, 2018b, 2019a, 2019b, 2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3 | | align="center" | 2014a, 2016b, 2017a, 2018a, 2018b, 2019a, 2019b, 2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3 | ||
| 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: | | Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab URL: http://www.mathworks.com/products/matlab Keyword:tools<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://maven.apache.org/index.html maven] | | align="center" | [https://maven.apache.org/index.html maven] | ||
| Line 1,398: | Line 1,398: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.12.1 | | 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 | | <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" | [http://metagene.nig.ac.jp/ metageneannotator] | ||
| Line 1,418: | Line 1,418: | ||
| align="center" | math | | align="center" | math | ||
| align="center" | 4.0.3, 5.1.0 | | 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 | | <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" | [https://github.com/codeandkey/mii mii] | ||
| Line 1,468: | Line 1,468: | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 3.0.0, 3.0.3, 3.1.3 | | 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: | | <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" | [http://www.mpich.org/ mpich] | ||
| Line 1,478: | Line 1,478: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 3.2.6 | | 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. | | <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" | [http://sobereva.com/multiwfn/ multiwfn] | ||
| Line 1,560: | Line 1,560: | ||
| <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> | | <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" | [ | | align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf] | ||
| align="center" | io | | align="center" | io | ||
| align="center" | 4.4.1.1, 4.6.1, 4.7.4 | | 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: | | <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" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++] | ||
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| align="center" | io | | align="center" | io | ||
| align="center" | 4.2 | | align="center" | 4.2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | | <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" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-c++4-mpi] | ||
| align="center" | io | | align="center" | io | ||
| align="center" | 4.3.0 | | 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. | | <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" | [http://www.unidata.ucar.edu/software/netcdf/ netcdf-fortran] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ URL: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/ URL: http://www.unidata.ucar.edu/software/netcdf/ Keyword:io<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [ | | align="center" | [https://www.unidata.ucar.edu/software/netcdf/ netcdf-mpi] | ||
| align="center" | io | | align="center" | io | ||
| align="center" | 4.1.3, 4.4.1.1, 4.6.1, 4.7.4 | | 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: | | <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" | [http://www.lysator.liu.se/~nisse/nettle/ nettle] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains networkx for different Python versions Homepage: http://python.org/ Keyword:tools<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains networkx for different Python versions Homepage: http://python.org/ Keyword:tools<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://www.nextflow.io | | align="center" | [https://www.nextflow.io nextflow] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 19.04.0, 19.10.0, 20.04.1, 20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3 | | align="center" | 19.04.0, 19.10.0, 20.04.1, 20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8, 23.04.3 | ||
| <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 | | <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" | [http://cibiv.github.io/NextGenMap/ nextgenmap] | ||
| Line 1,717: | Line 1,717: | ||
| align="center" | [https://www.openfoam.com/ openfoam] | | align="center" | [https://www.openfoam.com/ openfoam] | ||
| align="center" | phys | | align="center" | phys | ||
| align="center" | | | align="center" | 2.2.2, 2.3.1, 2.4.0, 3.0.1, 4.1, 5.0, 6, 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> | | 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> | ||
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| Line 1,788: | Line 1,788: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.0.9 | | align="center" | 2.0.9 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage | | <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" | [https://github.com/imageworks/OpenShadingLanguage osl] | ||
| Line 1,933: | Line 1,933: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.22, 1.23, 1.24 | | align="center" | 1.22, 1.23, 1.24 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Pilon is an automated genome assembly improvement and variant detection tool | | <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" | [http://www.well.ox.ac.uk/platypus platypus] | ||
| Line 1,942: | Line 1,942: | ||
| align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink] | | align="center" | [http://pngu.mgh.harvard.edu/~purcell/plink/ plink] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | | | 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> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. Homepage: http://pngu.mgh.harvard.edu/~purcell/plink/ Keyword:bio<br /><br /><br /></div> | ||
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| Line 1,993: | Line 1,993: | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.6.3 | | 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 | | <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" | [ | | align="center" | [https://proj.org proj] | ||
| align="center" | geo | | align="center" | geo | ||
| align="center" | 4.9.3, 6.0.0, 6.3.0, 7.0.0 | | 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: | | <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" | [https://github.com/google/protobuf/ protobuf] | ||
| Line 2,013: | Line 2,013: | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 6.1.2, 6.2.5, 7.0.1, 7.4.0 | | align="center" | 6.1.2, 6.2.5, 7.0.1, 7.4.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: pytest: simple powerful testing with Python Homepage: https://pytest.org URL: https://pytest.org Compatible modules: python/3.7, python/3.8, python/3.9, python/3.10 Extensions: | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: pytest: simple powerful testing with Python Homepage: https://pytest.org URL: https://pytest.org Compatible modules: python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Extensions: iniconfig-2.0.0, packaging-23.1, pluggy-1.2.0, py-1.11.0, pytest-7.4.0, tomli-2.0.1<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://python.org/ python] | | align="center" | [https://python.org/ python] | ||
| Line 2,073: | Line 2,073: | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 3.3.8, 4.8.7, 5.6.1, 5.9.6, 5.10.1, 5.11.3, 5.12.3, 5.12.8, 5.13.1 | | 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/ | | <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> | ||
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| align="center" | [https://www.synopsys.com/silicon/quantumatk.html quantumatk] | | align="center" | [https://www.synopsys.com/silicon/quantumatk.html quantumatk] | ||
| Line 2,095: | Line 2,095: | ||
| <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> | | <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/ | | align="center" | [https://github.com/isovic/racon/ racon] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.4.13, 20170719 | | 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/ | | <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" | [http://randomlib.sourceforge.net/html/ randomlib] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.2.0 | | 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. | | <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" | [https://bix.ucsd.edu/repeatscout/ repeatscout] | ||
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| align="center" | tools | | align="center" | tools | ||
| align="center" | 5.34.36, 6.08.02, 6.14.04 | | 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 | | <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" | [https://www.rosettacommons.org rosetta] | ||
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| align="center" | math | | align="center" | math | ||
| align="center" | 2017b, 2018b, 2019a, 2019b, 2020a, 2020b, 2021a, 2022a, 2023a, 2023b | | align="center" | 2017b, 2018b, 2019a, 2019b, 2020a, 2020b, 2021a, 2022a, 2023a, 2023b | ||
| Documentation: [[Python]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bundle which contains the Scientific Python stack, including Cycler, mpmath, numpy, scipy, sympy, pandas, matplotlib, ipython_genutils, traitlets, ptyprocess, pathlib2, pickleshare, pexpect, simplegeneric, ipython, ipykernel, jupyter_client, jupyter_core, pyzmq, tornado, futures and ipyparallel. Homepage: http://python.org/ URL: http://python.org/ Compatible modules: | | 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" | [https://gforge.inria.fr/projects/scotch/ scotch] | ||
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| align="center" | math | | align="center" | math | ||
| align="center" | 5.1.1, 5.2.1 | | 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. | | <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" | [https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome supernova] | ||
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| align="center" | - | | align="center" | - | ||
| align="center" | 3.0.12, 4.0.1 | | 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/ | | <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" | [http://samtools.sourceforge.net tabix] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files for major operating systems including Windows, Linux, and Mac OS X, and can be directly used without any dependencies nor local database buiding. Homepage: https://bioinf.shenwei.me/taxonkit/ URL: https://bioinf.shenwei.me/taxonkit/<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data. It provides executable binary files for major operating systems including Windows, Linux, and Mac OS X, and can be directly used without any dependencies nor local database buiding. Homepage: https://bioinf.shenwei.me/taxonkit/ URL: https://bioinf.shenwei.me/taxonkit/<br /><br /><br /></div> | ||
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| align="center" | [ | | align="center" | [https://github.com/oneapi-src/oneTBB tbb] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2017.2.132 | | align="center" | 2018_U5, 2017.2.132, 2020.2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel Threading Building Blocks | | <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> | ||
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| align="center" | [https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ tbl2asn] | | align="center" | [https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ tbl2asn] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.0c | | align="center" | 2.0c | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: TMHMM 2.0 predicts transmembrane helices in proteins. The method is described in: Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes. Anders Krogh and Bjorn Larsson, Gunnar von Heijne, and Erik L.L. Sonnhammer. J. Mol. Biol. 305:567-580, 2001. and: A hidden Markov model for predicting transmembrane helices in protein sequences. Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh. In J. Glasgow et al., eds.: Proc. of ISMB6, pages 175-182. AAAI Press, 1998. Homepage | | <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> | ||
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| align="center" | [http://ccb.jhu.edu/software/tophat/ tophat] | | align="center" | [http://ccb.jhu.edu/software/tophat/ tophat] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.4.0, 2.5.0, 2.8.4 | | 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. | | <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> | ||
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| align="center" | [https://trinotate.github.io/ trinotate] | | align="center" | [https://trinotate.github.io/ trinotate] | ||
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| <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> | | <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> | ||
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| align="center" | [ | | align="center" | [http://www.unidata.ucar.edu/software/udunits/ udunits] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2.2.24, 2.2.26 | | 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: | | <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: http://www.unidata.ucar.edu/software/udunits/ Keyword:tools<br /><br /><br /></div> | ||
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| align="center" | [https://www.unixodbc.org unixodbc] | | align="center" | [https://www.unixodbc.org unixodbc] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org Keyword:vis<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. Homepage: http://www.vtk.org Keyword:vis<br /><br /><br /></div> | ||
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| align="center" | [https://software.intel.com/ | | align="center" | [https://software.intel.com/en-us/vtune vtune] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2018.3, 2019.3, 2020.1, 2022.2 | | align="center" | 2018.3, 2019.3, 2020.1, 2022.2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Intel VTune | | <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> | ||
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| align="center" | [https://code.ornl.gov/neams-workbench/wasp wasp] | | align="center" | [https://code.ornl.gov/neams-workbench/wasp wasp] | ||