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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" | [https://dalexander.github.io/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: https://dalexander.github.io/admixture/ URL: https://dalexander.github.io/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" | | | align="center" | 18.14-18.17, 22.5-23.5, 20.12-20.15, 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> | ||
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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" | [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, 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, 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://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 | | 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 | | 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" | [https://github.com/NVIDIA/gdrcopy gdrcopy] | | align="center" | [https://github.com/NVIDIA/gdrcopy gdrcopy] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 2.1, 2.3.1, 2.4.1 | | align="center" | 2.1, 2.3, 2.3.1, 2.4.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. Homepage: https://github.com/NVIDIA/gdrcopy URL: https://github.com/NVIDIA/gdrcopy<br /><br /><br /></div> | ||
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| align="center" | [http://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 | | 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" | 2020.5-RAMD-2.0, 2024.1-RAMD-2.1 | | align="center" | 2020.5-RAMD-2.0, 2024.1-RAMD-2.1 | ||
| | | <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] | ||
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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" | 5.55-88.0, 5.50-84.0, 5.63-95.0, 5.64-96.0, 5.56-89.0, 5.53-87.0, 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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| align="center" | [http://openjdk.java.net java] | | align="center" | [http://openjdk.java.net java] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | | | align="center" | 1.8.0_192, 1.8.0_292, 11.0.16_8, 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 | | <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> | ||
|- | |- | ||
| 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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| align="center" | [https://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" | | | align="center" | R2022b, R2024a, R2020b, R2021b | ||
| 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> | | 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" | 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" | 14-7e284 | | align="center" | 15-6f452, 14-7e284, 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" | 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> | ||
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| align="center" | [https://openbabel.org openbabel-omp] | | align="center" | [https://openbabel.org openbabel-omp] | ||
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| align="center" | [http://www.openmx-square.org/ openmx] | | align="center" | [http://www.openmx-square.org/ openmx] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | | | align="center" | 3.9.9 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/ Keyword:chem<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/ Keyword:chem<br /><br /><br /></div> | ||
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| 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" | | | align="center" | 2.00-10252019-avx2, 2.00a3.6, 2.00a5.8, 1.9b_6.21-x86_64, 2.00-20231024-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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| 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] | ||
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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" | [ | | align="center" | [http://qwt.sourceforge.net/ 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: | | <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> | ||
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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:// | | align="center" | [https://www3.mrc-lmb.cam.ac.uk/relion/ 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:// | | <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> | ||
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| align="center" | [https://repast.github.io/ repasthpc] | | align="center" | [https://repast.github.io/ repasthpc] | ||
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| align="center" | [https://www.htslib.org/ samtools] | | align="center" | [https://www.htslib.org/ samtools] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 0.1.20, 1.10, 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, 1.20 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | - | | 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: | | <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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| align="center" | - | | align="center" | - | ||
| align="center" | 0.13.0, 0.14.2, 0.16.0, 0.18.1, 0.19.0 | | align="center" | 0.13.0, 0.14.2, 0.16.0, 0.18.1, 0.19.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.10, python/3.11<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Apache Thrift software framework, for scalable cross-language services development, combines a software stack with a code generation engine to build services that work efficiently and seamlessly between C++, Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages. Homepage: https://thrift.apache.org/ URL: https://thrift.apache.org/ Compatible modules: python/3.10, python/3.11, python/3.12<br /><br /><br /></div> | ||
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| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm] | | align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm] | ||