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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" | [https://dalexander.github.io/admixture/ admixture]
| 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: https://dalexander.github.io/admixture/ URL: https://dalexander.github.io/admixture/ Keyword:bio<br /><br /><br /></div>
| <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" | [http://ambermd.org/amber.html amber]
| align="center" | [https://ambermd.org/amber.html amber]
| align="center" | chem
| align="center" | chem
| align="center" | 18.14-18.17, 20.12-20.15, 20.9-20.15, 22.5-23.5
| 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: http://ambermd.org/amber.html URL: http://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: https://ambermd.org/amber.html URL: https://ambermd.org/amber.html Keyword:chem<br /><br /><br /></div>
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| align="center" | [https://ambermd.org/AmberTools.php ambertools]
| align="center" | [https://ambermd.org/AmberTools.php ambertools]
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| align="center" | [http://www.ansys.com ansys]
| align="center" | [http://www.ansys.com ansys]
| align="center" | phys
| align="center" | phys
| align="center" | 2024R1.03, 2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2
| align="center" | 2024R1.03, 2019R3, 2020R2, 2021R1, 2021R2, 2022R1, 2022R2, 2023R1, 2023R2, 2024R1
| 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>
| 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" | [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, 1.0.0, 2.0.0, 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
| 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://github.com/infphilo/centrifuge centrifuge]
| align="center" | [https://github.com/infphilo/centrifuge centrifuge]
| align="center" | bio
| align="center" | bio
| align="center" | 1.0.4-beta, 1.0.4
| align="center" | 1.0.4-beta
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge URL: https://github.com/infphilo/centrifuge Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers Homepage: https://github.com/infphilo/centrifuge URL: https://github.com/infphilo/centrifuge Keyword:bio<br /><br /><br /></div>
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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, 6.1.0.357, 6.2.0.415
| align="center" | 5.6, 6.0.0.405, 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" | 2020-11-14, 2019-09-12
| align="center" | 2019-09-12, 2020-11-14
| <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" | chem
| align="center" | chem
| align="center" | 2016.6, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023.2, 2023.3, 2024.1
| align="center" | 2016.6, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023.2, 2023.3, 2024.1
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a CPU only build, containing both MPI and threadMPI builds. Homepage: http://www.gromacs.org URL: http://www.gromacs.org Keyword:chem<br /><br /><br /></div>
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| align="center" | [http://colvars.github.io/ gromacs-colvars]
| align="center" | [http://colvars.github.io/ gromacs-colvars]
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| align="center" | chem
| align="center" | chem
| align="center" | 2020.5-RAMD-2.0, 2024.1-RAMD-2.1
| align="center" | 2020.5-RAMD-2.0, 2024.1-RAMD-2.1
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been modified to support RAMD, which is used to identify ligand exit routes from the buried binding pockets of receptors and investigate the mechanism of ligand dissociation. https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ This is a CPU only build, containing both MPI and threadMPI builds. CC-Wiki: GROMACS Homepage: https://github.com/HITS-MCM/gromacs-ramd URL: https://github.com/HITS-MCM/gromacs-ramd Keyword:chem<br /><br /><br /></div>
| <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 modified to support RAMD, which is used to identify ligand exit routes from the buried binding pockets of receptors and investigate the mechanism of ligand dissociation. https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ This is a CPU only build, containing both MPI and threadMPI builds. Homepage: https://github.com/HITS-MCM/gromacs-ramd URL: https://github.com/HITS-MCM/gromacs-ramd Keyword:chem<br /><br /><br /></div>
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| align="center" | [https://cbjh.gitlab.io/gromacs-swaxs-docs/ gromacs-swaxs]
| align="center" | [https://cbjh.gitlab.io/gromacs-swaxs-docs/ gromacs-swaxs]
| align="center" | chem
| align="center" | chem
| align="center" | 2021.7-0.5.1
| align="center" | 2021.7-0.5.1
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a CPU only build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: https://cbjh.gitlab.io/gromacs-swaxs-docs/ URL: https://cbjh.gitlab.io/gromacs-swaxs-docs/ Keyword:chem<br /><br /><br /></div>
| Documentation: [[GROMACS]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Modified GROMACS for small-angle scattering calculations (SAXS/WAXS/SANS). This is a GPU enabled build, containing both MPI and threadMPI builds. - CC-Wiki: GROMACS Homepage: https://cbjh.gitlab.io/gromacs-swaxs-docs/ URL: https://cbjh.gitlab.io/gromacs-swaxs-docs/ Keyword:chem<br /><br /><br /></div>
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| align="center" | [https://www.gnu.org/software/gsl/ gsl]
| align="center" | [https://www.gnu.org/software/gsl/ gsl]
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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" | 5.56-89.0, 5.64-96.0, 5.53-87.0, 5.63-95.0, 5.55-88.0, 5.50-84.0, 5.52-86.0
| align="center" | 5.64-96.0, 5.55-88.0, 5.53-87.0, 5.56-89.0, 5.63-95.0, 5.50-84.0, 5.52-86.0
| <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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| <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" | [http://www.mathworks.com/products/compiler/mcr/ mcr]
| align="center" | [https://www.mathworks.com/products/compiler/mcr/ mcr]
| align="center" | tools
| align="center" | tools
| align="center" | R2024a, R2022b, R2021b, R2020b
| align="center" | R2022b, R2020b, R2021b, R2024a
| 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: http://www.mathworks.com/products/compiler/mcr/ URL: http://www.mathworks.com/products/compiler/mcr/ Keyword:tools<br /><br /><br /></div>
| 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 Compatible modules: Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Homepage: https://github.com/voutcn/megahit URL: https://github.com/voutcn/megahit 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, 14-7e284, 13-45111
| 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>
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| align="center" | [https://www.openfoam.com/ openfoam]
| align="center" | [https://www.openfoam.com/ openfoam]
| align="center" | phys
| align="center" | phys
| align="center" | 8, 9, 10, 11, v2006, v2012, v2112, v2206, v2212, v2306, v2312
| align="center" | 6, 8, 9, 10, v2006, v2012, v2112, v2206, v2212, v2306, v2312
| 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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| align="center" | chem
| align="center" | chem
| align="center" | 7.5.0, 7.6.0, 7.7.0, 8.0.0
| align="center" | 7.5.0, 7.6.0, 7.7.0, 8.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: pdbfixer-1.8.1 Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMM is a toolkit for molecular simulation. Homepage: http://openmm.org URL: http://openmm.org Compatible modules: python/3.10, python/3.11 Extensions: pdbfixer-1.8.1 Keyword:chem<br /><br /><br /></div>
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| align="center" | [http://openmm.org openmm-alphafold]
| align="center" | [http://openmm.org openmm-alphafold]
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| 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: 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>
| 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>
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| align="center" | [http://www.mcs.anl.gov/petsc petsc]
| align="center" | [http://www.mcs.anl.gov/petsc petsc]
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| align="center" | [https://www.cog-genomics.org/plink/1.9/ plink]
| align="center" | [https://www.cog-genomics.org/plink/1.9/ plink]
| align="center" | bio
| align="center" | bio
| align="center" | 2.00a3.6, 2.00-10252019-avx2, 2.00-20231024-avx2, 2.00a5.8, 1.9b_6.21-x86_64
| align="center" | 2.00a5.8, 2.00-10252019-avx2, 2.00-20231024-avx2, 2.00a3.6, 1.9b_6.21-x86_64
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ URL: https://www.cog-genomics.org/plink/1.9/ Keyword:bio<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: plink-1.9-x86_64: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/ URL: https://www.cog-genomics.org/plink/1.9/ Keyword:bio<br /><br /><br /></div>
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| align="center" | [http://www.portaudio.com/ portaudio]
| align="center" | [http://www.portaudio.com/ portaudio]
| align="center" | -
| align="center" | -
| align="center" | 190600_20161030, 190700_20210406
| 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/3.8, python/3.9, python/3.10 Extensions: PyAudio-0.2.13<br /><br /><br /></div>
| <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]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Homepage: https://github.com/ablab/quast URL: https://github.com/ablab/quast Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: joblib-0.17.0, QUAST-5.2.0, semantic-version-2.8.5, simplejson-3.17.0, toml-0.10.2<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Homepage: https://github.com/ablab/quast URL: https://github.com/ablab/quast Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: joblib-0.17.0, QUAST-5.2.0, semantic-version-2.8.5, simplejson-3.17.0, toml-0.10.2<br /><br /><br /></div>
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| align="center" | [http://qwt.sourceforge.net/ qwt]
| align="center" | [https://qwt.sourceforge.io/ qwt]
| align="center" | tools
| align="center" | tools
| align="center" | 6.1.4, 6.2.0
| align="center" | 6.1.4, 6.2.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: http://qwt.sourceforge.net/ URL: http://qwt.sourceforge.net/ Keyword:tools<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: https://qwt.sourceforge.io/ URL: https://qwt.sourceforge.io/ Keyword:tools<br /><br /><br /></div>
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| align="center" | [http://qwtpolar.sourceforge.net/ qwtpolar]
| align="center" | [http://qwtpolar.sourceforge.net/ qwtpolar]
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center. The method has the following properties It works on quantitative and binary traits, including binary traits with unbalanced case-control ratios It can process multiple phenotypes at once For binary traits it supports Firth logistic regression and an SPA test It can perform gene/region-based burden tests It is fast and memory efficient It supports the BGEN, PLINK bed/bim/fam and PLINK2 pgen/pvar/psam genetic data formats It is ideally suited for implementation in Apache Spark (see GLOW) Citation Mbatchou, J., Barnard, L., Backman, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat Genet 53, 10971103 (2021). https://doi.org/10.1038/s41588-021-00870-7 Homepage: https://rgcgithub.github.io/regenie/ URL: https://rgcgithub.github.io/regenie/<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: regenie is a C++ program for whole genome regression modelling of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center. The method has the following properties It works on quantitative and binary traits, including binary traits with unbalanced case-control ratios It can process multiple phenotypes at once For binary traits it supports Firth logistic regression and an SPA test It can perform gene/region-based burden tests It is fast and memory efficient It supports the BGEN, PLINK bed/bim/fam and PLINK2 pgen/pvar/psam genetic data formats It is ideally suited for implementation in Apache Spark (see GLOW) Citation Mbatchou, J., Barnard, L., Backman, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat Genet 53, 10971103 (2021). https://doi.org/10.1038/s41588-021-00870-7 Homepage: https://rgcgithub.github.io/regenie/ URL: https://rgcgithub.github.io/regenie/<br /><br /><br /></div>
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| align="center" | [https://www3.mrc-lmb.cam.ac.uk/relion/ relion]
| align="center" | [https://bitbucket.org/scheres/relion-3.0_beta.git relion]
| align="center" | chem
| align="center" | chem
| align="center" | 3.1.1, 4.0.0
| align="center" | 3.1.1, 4.0.0
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Homepage: https://www3.mrc-lmb.cam.ac.uk/relion/ URL: https://www3.mrc-lmb.cam.ac.uk/relion/ Keyword:chem<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. It is developed in the research group of Sjors Scheres at the MRC Laboratory of Molecular Biology. Homepage: https://bitbucket.org/scheres/relion-3.0_beta.git URL: https://bitbucket.org/scheres/relion-3.0_beta.git Keyword:chem<br /><br /><br /></div>
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| align="center" | [https://repast.github.io/ repasthpc]
| align="center" | [https://repast.github.io/ repasthpc]
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| align="center" | -
| align="center" | -
| align="center" | 8.6.1.6
| align="center" | 8.6.1.6
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NVIDIA TensorRT is a platform for high-performance deep learning inference Homepage: https://developer.nvidia.com/tensorrt URL: https://developer.nvidia.com/tensorrt Compatible modules: python/3.8, python/3.9, python/3.10, python/3.11<br /><br /><br /></div>
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: NVIDIA TensorRT is a platform for high-performance deep learning inference Homepage: https://developer.nvidia.com/tensorrt URL: https://developer.nvidia.com/tensorrt Compatible modules: python/3.10, python/3.11<br /><br /><br /></div>
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| align="center" | [https://github.com/tesseract-ocr/tesseract tesseract]
| align="center" | [https://github.com/tesseract-ocr/tesseract tesseract]
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