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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc<br /><br /><br /></div> | ||
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| align="center" | [ | | align="center" | [http://software.genetics.ucla.edu/admixture admixture] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.3.0 | | align="center" | 1.3.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: http://software.genetics.ucla.edu/admixture URL: http://software.genetics.ucla.edu/admixture Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://projects.coin-or.org/ADOL-C adol-c] | | align="center" | [https://projects.coin-or.org/ADOL-C adol-c] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT Homepage: https://github.com/ALPSCore/ALPSCore URL: https://github.com/ALPSCore/ALPSCore Keyword:phys<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The ALPSCore project, based on the ALPS (Algorithms and Libraries for Physics Simulations) project, provides generic algorithms and utilities for physics problems. It strives to increase software reuse in the physics community. For copyright see COPYRIGHT.TXT For licensing see LICENSE.TXT For acknowledgment in scientific publications see ACKNOWLEDGE.TXT Homepage: https://github.com/ALPSCore/ALPSCore URL: https://github.com/ALPSCore/ALPSCore Keyword:phys<br /><br /><br /></div> | ||
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| align="center" | [ | | align="center" | [https://ambermd.org/amber.html amber] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 20. | | align="center" | 20.12-20.15, 18.14-18.17, 22.5-23.5, 20.9-20.15 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: https://ambermd.org/amber.html URL: https://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://ambermd.org/AmberTools.php ambertools] | | align="center" | [https://ambermd.org/AmberTools.php ambertools] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 20, 21, 22 | | align="center" | 20, 21, 22, 23.5 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Homepage: https://ambermd.org/AmberTools.php URL: https://ambermd.org/AmberTools.php Keyword:chem<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Homepage: https://ambermd.org/AmberTools.php URL: https://ambermd.org/AmberTools.php Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [https://arrow.apache.org arrow] | | align="center" | [https://arrow.apache.org arrow] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 0.16.0, 0.17.1, 2.0.0, | | align="center" | 0.16.0, 0.17.1, 1.0.0, 2.0.0, 4.0.0, 5.0.0, 8.0.0, 9.0.0, 10.0.1, 11.0.0, 12.0.1, 13.0.0, 14.0.0, 14.0.1, 15.0.1, 16.1.0, 17.0.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.12, python/3.11, python/3.10 Keyword:tools<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.12, python/3.11, python/3.10 Keyword:tools<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] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | | | align="center" | 5.4-240301 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Homepage: https://faculty.washington.edu/browning/beagle/beagle.html URL: https://faculty.washington.edu/browning/beagle/beagle.html<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Homepage: https://faculty.washington.edu/browning/beagle/beagle.html URL: https://faculty.washington.edu/browning/beagle/beagle.html<br /><br /><br /></div> | ||
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| align="center" | [https://ccb.jhu.edu/software/bracken/ bracken] | | align="center" | [https://ccb.jhu.edu/software/bracken/ bracken] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 2.6.0, 2.7 | | align="center" | 2.6.0, 2.7, 3.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. Homepage: https://ccb.jhu.edu/software/bracken/ URL: https://ccb.jhu.edu/software/bracken/<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. Homepage: https://ccb.jhu.edu/software/bracken/ URL: https://ccb.jhu.edu/software/bracken/<br /><br /><br /></div> | ||
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| align="center" | [https://www.comsol.com comsol] | | align="center" | [https://www.comsol.com comsol] | ||
| align="center" | phys | | align="center" | phys | ||
| align="center" | 5.6, 6.0.0.405, 6.1.0.357, 6.2, 6.2.0.415 | | align="center" | 5.6, 6.0.0.405, 6.1, 6.1.0.357, 6.2, 6.2.0.415 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com URL: https://www.comsol.com Keyword:phys<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com URL: https://www.comsol.com Keyword:phys<br /><br /><br /></div> | ||
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| align="center" | [http://research-pub.gene.com/gmap/ gmap-gsnap] | | align="center" | [http://research-pub.gene.com/gmap/ gmap-gsnap] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2019-09-12 | | align="center" | 2020-11-14, 2019-09-12 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program Homepage: http://research-pub.gene.com/gmap/ URL: http://research-pub.gene.com/gmap/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program Homepage: http://research-pub.gene.com/gmap/ URL: http://research-pub.gene.com/gmap/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [http://www.gromacs.org gromacs] | | align="center" | [http://www.gromacs.org gromacs] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023.2, 2023.3, 2024.1 | | align="center" | 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2, 2023.3, 2024.1 | ||
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a | | Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [http://colvars.github.io/ gromacs-colvars] | | align="center" | [http://colvars.github.io/ gromacs-colvars] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 2020.6 | | align="center" | 2020.6 | ||
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been patched with 'Colvars', a collective variables module for molecular simulation programs. This is a | | Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been patched with 'Colvars', a collective variables module for molecular simulation programs. This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: http://colvars.github.io/ URL: http://colvars.github.io/ Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [https://www.cp2k.org/tools:gromacs gromacs-cp2k] | | align="center" | [https://www.cp2k.org/tools:gromacs gromacs-cp2k] | ||
| Line 1,728: | Line 1,728: | ||
| align="center" | io | | align="center" | io | ||
| align="center" | 1.8.22, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2 | | align="center" | 1.8.22, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11 Extensions: blosc2-2.2.9, cached-property-1.5.2, h5py-3.10.0, ndindex-1.7, numexpr-2.8.7, py-cpuinfo-9.0.0, tables-3.9.1 Keyword:io<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. Homepage: https://portal.hdfgroup.org/display/support URL: https://portal.hdfgroup.org/display/support Compatible modules: python/3.10, python/3.11 Extensions: blosc2-2.2.9, cached-property-1.5.2, h5py-3.10.0, hdf5-blosc-1.0.1, ndindex-1.7, numexpr-2.8.7, py-cpuinfo-9.0.0, tables-3.9.1 Keyword:io<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi] | | align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi] | ||
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| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan] | | align="center" | [http://www.ebi.ac.uk/interpro/ interproscan] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 5. | | align="center" | 5.63-95.0, 5.55-88.0, 5.64-96.0, 5.53-87.0, 5.56-89.0, 5.52-86.0, 5.50-84.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan_data] | | align="center" | [http://www.ebi.ac.uk/interpro/ interproscan_data] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 5. | | align="center" | 5.64-96.0, 5.63-95.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/<br /><br /><br /></div> | ||
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| align="center" | [http://openjdk.java.net java] | | align="center" | [http://openjdk.java.net java] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | | | align="center" | 11.0.16_8, 1.8.0_192, 1.8.0_292, 11.0.22, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1 | ||
| Documentation: [[Java]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://openjdk.java.net URL: http://openjdk.java.net Keyword:tools<br /><br /><br /></div> | | Documentation: [[Java]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://openjdk.java.net URL: http://openjdk.java.net Keyword:tools<br /><br /><br /></div> | ||
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| align="center" | - | | align="center" | - | ||
| align="center" | 1.1.0 | | align="center" | 1.1.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores. Homepage: https://git.osgeo.org/gitea/rttopo/librttopo URL: https://git.osgeo.org/gitea/rttopo/librttopo<br /><br /><br /></div> | ||
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| align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9] | | align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9] | ||
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| align="center" | [http://www.mathworks.com/products/matlab matlab] | | align="center" | [http://www.mathworks.com/products/matlab matlab] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 2020a | | align="center" | 2020a, 2020b.4, 2020b.6, 2021a.1, 2021a.5, 2021b.3, 2022a, 2022b.2, 2023a.3, 2023b.2 | ||
| Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab URL: http://www.mathworks.com/products/matlab Keyword:tools<br /><br /><br /></div> | | Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. Homepage: http://www.mathworks.com/products/matlab URL: http://www.mathworks.com/products/matlab Keyword:tools<br /><br /><br /></div> | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ URL: http://micans.org/mcl/ Keyword:math<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ URL: http://micans.org/mcl/ Keyword:math<br /><br /><br /></div> | ||
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| align="center" | [ | | align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | | | align="center" | R2020b, R2024a, R2021b, R2022b | ||
| Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: | | Documentation: [[MATLAB]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. Homepage: https://www.mathworks.com/products/compiler/mcr/ URL: https://www.mathworks.com/products/compiler/mcr/ Keyword:tools<br /><br /><br /></div> | ||
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| align="center" | [https://grimme-lab.github.io/mctc-lib mctc-lib] | | align="center" | [https://grimme-lab.github.io/mctc-lib mctc-lib] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.2.9 | | align="center" | 1.2.9 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Homepage: https://github.com/voutcn/megahit URL: https://github.com/voutcn/megahit | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Homepage: https://github.com/voutcn/megahit URL: https://github.com/voutcn/megahit Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [http://meme-suite.org meme] | | align="center" | [http://meme-suite.org meme] | ||
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| align="center" | [https://mmseqs.com mmseqs2] | | align="center" | [https://mmseqs.com mmseqs2] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 15-6f452 | | align="center" | 14-7e284, 15-6f452, 13-45111 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com<br /><br /><br /></div> | ||
|- | |- | ||
| Line 2,933: | Line 2,933: | ||
| align="center" | math | | align="center" | math | ||
| align="center" | 2.6.1, 2.6.2, 2.7.0, 2.7.1 | | align="center" | 2.6.1, 2.6.2, 2.7.0, 2.7.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt URL: http://ab-initio.mit.edu/wiki/index.php/NLopt Compatible modules: python/3.10, python/3.10, python/3.10, python/3.10, python/3.11, python/3.11, python/3.11, python/3.11 Keyword:math<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://nodejs.org nodejs] | | align="center" | [https://nodejs.org nodejs] | ||
| Line 3,033: | Line 3,033: | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 3.1.1 | | align="center" | 3.1.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Homepage: https://openbabel.org URL: https://openbabel.org Compatible modules: python/3.6, python/3.7, python/3.8, python/3.9, python/3.10, python/3.11 Extensions: openbabel-3.1.1.1 Keyword:chem<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [http://www.openblas.net/ openblas] | | align="center" | [http://www.openblas.net/ openblas] | ||
| Line 3,353: | Line 3,353: | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 5.30.2, 5.36.1 | | align="center" | 5.30.2, 5.36.1 | ||
| Documentation: [[Perl]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Carp-1.50, constant-1.33, Data::Dumper-2.183, Exporter-5.77, File::Path-2.18, File::Spec-3.75, Getopt::Long-2.54, IO::File-1.51, Text::ParseWords-3.31, Thread::Queue-3.13, threads-2.21 Keyword:tools<br /><br /><br /></div> | | Documentation: [[Perl]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality. Homepage: https://www.perl.org/ URL: https://www.perl.org/ Extensions: Algorithm::Dependency-1.112, Algorithm::Diff-1.201, aliased-0.34, AnyEvent-7.17, App::Cmd-0.335, App::cpanminus-1.7046, AppConfig-1.71, Archive::Extract-0.88, Array::Transpose-0.06, Array::Utils-0.5, Authen::NTLM-1.09, Authen::SASL-2.16, AutoLoader-5.74, B::COW-0.007, B::Hooks::EndOfScope-0.26, B::Lint-1.20, boolean-0.46, Business::ISBN-3.008, Business::ISBN::Data-20230516.001, Canary::Stability-2013, Capture::Tiny-0.48, Carp-1.50, Carp::Clan-6.08, Carp::Heavy-1.50, CGI-4.57, Class::Accessor-0.51, Class::Data::Inheritable-0.09, Class::DBI-v3.0.17, Class::DBI::SQLite-0.11, Class::Inspector-1.36, Class::ISA-0.36, Class::Load-0.25, Class::Load::XS-0.10, Class::Method::Modifiers-2.15, Class::Singleton-1.6, Class::Tiny-1.008, Class::Trigger-0.15, Class::XSAccessor-1.19, Clone-0.46, Clone::Choose-0.010, common::sense-3.75, Compress::Raw::Zlib-2.204, Config::General-2.65, Config::INI-0.029, Config::MVP-2.200013, Config::MVP::Reader::INI-2.101465, Config::Simple-4.58, Config::Tiny-2.29, Const::Exporter-1.2.2, Const::Fast-0.014, constant-1.33, CPAN::Meta::Check-0.017, CPAN::Uploader-0.103018, CPANPLUS-0.9914, Crypt::DES-2.07, Crypt::Rijndael-1.16, Cwd-3.75, Cwd::Guard-0.05, Data::Dump-1.25, Data::Dumper-2.183, Data::Dumper::Concise-2.023, Data::Grove-0.08, Data::OptList-0.114, Data::Section-0.200008, Data::Section::Simple-0.07, Data::Stag-0.14, Data::Types-0.17, Data::UUID-1.226, Date::Handler-1.2, Date::Language-2.33, DateTime-1.59, DateTime::Locale-1.38, DateTime::TimeZone-2.60, DateTime::Tiny-1.07, DBD::CSV-0.60, DBD::SQLite-1.72, DBI-1.643, DBIx::Admin::CreateTable-2.11, DBIx::Admin::DSNManager-2.02, DBIx::Admin::TableInfo-3.04, DBIx::ContextualFetch-1.03, DBIx::Simple-1.37, Devel::CheckCompiler-0.07, Devel::CheckLib-1.16, Devel::Cycle-1.12, Devel::FindPerl-0.016, Devel::GlobalDestruction-0.14, Devel::OverloadInfo-0.007, Devel::Size-0.83, Devel::StackTrace-2.04, Digest::HMAC-1.04, Digest::MD5::File-0.08, Digest::SHA1-2.13, Dist::CheckConflicts-0.11, Dist::Zilla-6.030, Email::Date::Format-1.008, Encode-3.19, Encode::Locale-1.05, Error-0.17029, Eval::Closure-0.14, Exception::Class-1.45, Expect-1.35, Exporter-5.77, Exporter::Declare-0.114, Exporter::Tiny-1.006002, ExtUtils::CBuilder-0.280236, ExtUtils::Config-0.008, ExtUtils::Constant-0.25, ExtUtils::CppGuess-0.26, ExtUtils::Helpers-0.026, ExtUtils::InstallPaths-0.012, ExtUtils::MakeMaker-7.70, ExtUtils::ParseXS-3.44, Fennec::Lite-0.004, File::CheckTree-4.42, File::Copy::Recursive-0.45, File::Copy::Recursive::Reduced-0.006, File::Find::Rule-0.34, File::Find::Rule::Perl-1.16, File::Grep-0.02, File::HomeDir-1.006, File::Listing-6.15, File::Next-1.18, File::Path-2.18, File::pushd-1.016, File::Remove-1.61, File::ShareDir-1.118, File::ShareDir::Install-0.14, File::Slurp-9999.32, File::Slurp::Tiny-0.004, File::Slurper-0.014, File::Spec-3.75, File::Temp-0.2311, File::Which-1.27, Font::TTF-1.06, Getopt::Long-2.54, Getopt::Long::Descriptive-0.111, Git-0.42, GO-0.04, GO::Utils-0.15, Graph-0.9726, Graph::ReadWrite-2.10, Hash::Merge-0.302, Hash::Objectify-0.008, Heap-0.80, Hook::LexWrap-0.26, HTML::Entities::Interpolate-1.10, HTML::Form-6.11, HTML::Parser-3.81, HTML::Tagset-3.20, HTML::Template-2.97, HTML::Tree-5.07, HTTP::CookieJar-0.014, HTTP::Cookies-6.10, HTTP::Daemon-6.16, HTTP::Date-6.05, HTTP::Message-6.44, HTTP::Negotiate-6.01, HTTP::Tiny-0.082, if-0.0608, Ima::DBI-0.35, Import::Into-1.002005, Importer-0.026, Inline-0.86, IO::Compress::Zip-2.204, IO::File-1.51, IO::HTML-1.004, IO::Socket::SSL-2.083, IO::String-1.08, IO::Stringy-2.113, IO::TieCombine-1.005, IO::Tty-1.17, IO::Tty-1.17, IPC::Cmd-1.04, IPC::Run-20220807.0, IPC::Run3-0.048, IPC::System::Simple-1.30, JSON-4.10, JSON::MaybeXS-1.004005, JSON::XS-4.03, Lingua::EN::PluralToSingular-0.21, List::AllUtils-0.19, List::MoreUtils-0.430, List::MoreUtils::XS-0.430, List::SomeUtils-0.59, List::UtilsBy-0.12, local::lib-2.000029, Locale::Maketext::Simple-0.21, Log::Dispatch-2.71, Log::Dispatch::Array-1.005, Log::Dispatchouli-3.002, Log::Handler-0.90, Log::Log4perl-1.57, Log::Message-0.08, Log::Message::Simple-0.10, Log::Report-1.34, Log::Report::Optional-1.07, Logger::Simple-2.0, LWP::MediaTypes-6.04, LWP::Protocol::https-6.10, LWP::Simple-6.70, Mail::Util-2.21, Math::Bezier-0.01, Math::CDF-0.1, Math::Round-0.07, Math::Utils-1.14, Math::VecStat-0.08, MCE::Mutex-1.884, Meta::Builder-0.004, MIME::Base64-3.16, MIME::Charset-v1.013.1, MIME::Lite-3.033, MIME::Types-2.24, Mixin::Linewise::Readers-0.111, Mock::Quick-1.111, Module::Build-0.4234, Module::Build::Tiny-0.045, Module::Build::XSUtil-0.19, Module::CoreList-5.20230423, Module::Implementation-0.09, Module::Install-1.21, Module::Load-0.36, Module::Load::Conditional-0.74, Module::Metadata-1.000038, Module::Path-0.19, Module::Path-0.19, Module::Pluggable-5.2, Module::Runtime-0.016, Module::Runtime::Conflicts-0.003, Moo-2.005005, Moose-2.2203, MooseX::LazyRequire-0.11, MooseX::OneArgNew-0.007, MooseX::Role::Parameterized-1.11, MooseX::SetOnce-0.203, MooseX::Types-0.50, MooseX::Types::Perl-0.101344, Mouse-v2.5.10, Mozilla::CA-20221114, MRO::Compat-0.15, namespace::autoclean-0.29, namespace::clean-0.27, Net::Domain-3.15, Net::HTTP-6.22, Net::SMTP::SSL-1.04, Net::SNMP-v6.0.1, Net::SSLeay-1.92, Number::Compare-0.03, Number::Format-1.75, Object::Accessor-0.48, Object::InsideOut-4.05, Object::InsideOut-4.05, Package::Constants-0.06, Package::DeprecationManager-0.18, Package::Stash-0.40, Package::Stash::XS-0.30, PadWalker-2.5, Parallel::ForkManager-2.02, Params::Check-0.38, Params::Util-1.102, Params::Validate-1.31, Params::ValidationCompiler-0.31, parent-0.241, Parse::RecDescent-1.967015, Parse::Yapp-1.21, Path::Tiny-0.144, PDF::API2-2.044, Perl::OSType-1.010, Perl::PrereqScanner-1.100, PerlIO::utf8_strict-0.010, Pod::Elemental-0.103006, Pod::Escapes-1.07, Pod::Eventual-0.094003, Pod::LaTeX-0.61, Pod::Man-5.01, Pod::Parser-1.66, Pod::Plainer-1.04, Pod::POM-2.01, Pod::Simple-3.45, Pod::Weaver-4.019, PPI-1.276, Readonly-2.05, Ref::Util-0.204, Regexp::Common-2017060201, Role::HasMessage-0.007, Role::Identifiable::HasIdent-0.009, Role::Tiny-2.002004, Scalar::Util-1.63, Scalar::Util::Numeric-0.40, Scope::Guard-0.21, Set::Array-0.30, Set::IntervalTree-0.12, Set::IntSpan-1.19, Set::IntSpan::Fast-1.15, Set::Object-1.42, Set::Scalar-1.29, Shell-0.73, Socket-2.036, Software::License-0.104003, Specio-0.48, Spiffy-0.46, SQL::Abstract-2.000001, SQL::Statement-1.414, Statistics::Basic-1.6611, Statistics::Descriptive-3.0800, Storable-3.25, strictures-2.000006, String::Errf-0.009, String::Flogger-1.101246, String::Formatter-1.235, String::Print-0.94, String::RewritePrefix-0.009, String::Truncate-1.100603, String::TtyLength-0.03, Sub::Exporter-0.989, Sub::Exporter::ForMethods-0.100055, Sub::Exporter::GlobExporter-0.006, Sub::Exporter::Progressive-0.001013, Sub::Identify-0.14, Sub::Info-0.002, Sub::Install-0.929, Sub::Name-0.27, Sub::Quote-2.006008, Sub::Uplevel-0.2800, SVG-2.87, Switch-2.17, Sys::Info-0.7811, Sys::Info::Base-0.7807, Sys::Info::Driver::Linux-0.7905, Sys::Info::Driver::Linux::Device::CPU-0.7905, Sys::Info::Driver::Unknown-0.79, Sys::Info::Driver::Unknown::Device::CPU-0.79, Template-3.101, Template::Plugin::Number::Format-1.06, Term::Encoding-0.03, Term::ReadKey-2.38, Term::ReadLine::Gnu-1.45, Term::Table-0.016, Term::UI-0.50, Test-1.26, Test2::Plugin::NoWarnings-0.09, Test2::Require::Module-0.000155, Test::Base-0.89, Test::CheckDeps-0.010, Test::ClassAPI-1.07, Test::CleanNamespaces-0.24, Test::Deep-1.204, Test::Differences-0.69, Test::Exception-0.43, Test::FailWarnings-0.008, Test::Fatal-0.017, Test::File-1.993, Test::File::ShareDir::Dist-1.001002, Test::Harness-3.44, Test::LeakTrace-0.17, Test::Memory::Cycle-1.06, Test::More::UTF8-0.05, Test::Most-0.38, Test::Needs-0.002010, Test::NoWarnings-1.06, Test::Object-0.08, Test::Output-1.033, Test::Pod-1.52, Test::Requires-0.11, Test::RequiresInternet-0.05, Test::Simple-1.302195, Test::SubCalls-1.10, Test::Sys::Info-0.23, Test::Version-2.09, Test::Warn-0.37, Test::Warnings-0.031, Test::Without::Module-0.21, Test::YAML-1.07, Text::Aligner-0.16, Text::Balanced-2.06, Text::CSV-2.02, Text::CSV_XS-1.50, Text::Diff-1.45, Text::Format-0.62, Text::Glob-0.11, Text::Iconv-1.7, Text::ParseWords-3.31, Text::Soundex-3.05, Text::Table-1.135, Text::Table::Manifold-1.03, Text::Template-1.61, Thread::Queue-3.13, threads-2.21, Throwable-1.001, Tie::Function-0.02, Tie::IxHash-1.23, Time::HiRes-1.9764, Time::Local-1.35, Time::Piece-1.3401, Time::Piece::MySQL-0.06, Tree::DAG_Node-1.32, Try::Tiny-0.31, Type::Tiny-2.004000, Types::Serialiser-1.01, Types::Serialiser-1.01, Unicode::EastAsianWidth-12.0, Unicode::LineBreak-2019.001, UNIVERSAL::moniker-0.08, Unix::Processors-2.046, Unix::Processors-2.046, URI-5.19, Variable::Magic-0.63, version-0.9929, Want-0.29, WWW::RobotRules-6.02, XML::Bare-0.53, XML::DOM-1.46, XML::Filter::BufferText-1.01, XML::NamespaceSupport-1.12, XML::Parser-2.46, XML::RegExp-0.04, XML::SAX-1.02, XML::SAX::Base-1.09, XML::SAX::Expat-0.51, XML::SAX::Writer-0.57, XML::Simple-2.25, XML::Tiny-2.07, XML::Twig-3.52, XML::Writer-0.900, XML::XPath-1.48, XSLoader-0.24, YAML-1.30, YAML::Tiny-1.74 Keyword:tools<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [http://www.mcs.anl.gov/petsc petsc] | | align="center" | [http://www.mcs.anl.gov/petsc petsc] | ||
| Line 3,482: | Line 3,482: | ||
| align="center" | [https://www.cog-genomics.org/plink/2.0/ plink] | | align="center" | [https://www.cog-genomics.org/plink/2.0/ plink] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.9b_6.21-x86_64, 2.00- | | align="center" | 2.00a3.6, 1.9b_6.21-x86_64, 2.00-20231024-avx2, 2.00a5.8, 2.00-10252019-avx2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/2.0/ URL: https://www.cog-genomics.org/plink/2.0/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/2.0/ URL: https://www.cog-genomics.org/plink/2.0/ Keyword:bio<br /><br /><br /></div> | ||
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| Line 3,527: | Line 3,527: | ||
| align="center" | [http://www.portaudio.com/ portaudio] | | align="center" | [http://www.portaudio.com/ portaudio] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 190600_20161030 | | align="center" | 190700_20210406, 190600_20161030 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PortAudio is a free, cross-platform, open-source, audio I/O library. It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between developers on different platforms. Many applications use PortAudio for Audio I/O. Homepage: http://www.portaudio.com/ URL: http://www.portaudio.com/ Compatible modules: python/3. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PortAudio is a free, cross-platform, open-source, audio I/O library. It lets you write simple audio programs in 'C' or C++ that will compile and run on many platforms including Windows, Macintosh OS X, and Unix (OSS/ALSA). It is intended to promote the exchange of audio software between developers on different platforms. Many applications use PortAudio for Audio I/O. Homepage: http://www.portaudio.com/ URL: http://www.portaudio.com/ Compatible modules: python/3.6, python/3.7, python/3.8 Extensions: PyAudio-0.2.11<br /><br /><br /></div> | ||
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| align="center" | [https://www.postgresql.org/ postgresql] | | align="center" | [https://www.postgresql.org/ postgresql] | ||
| Line 4,022: | Line 4,022: | ||
| align="center" | [https://www.htslib.org/ samtools] | | align="center" | [https://www.htslib.org/ samtools] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 0.1.20, 1.10, 1.11, 1.12, 1.13, 1.15.1, 1.16.1, 1.17, 1.18 | | align="center" | 0.1.20, 1.10, 1.11, 1.12, 1.13, 1.15.1, 1.16.1, 1.17, 1.18 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div> | ||
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