41,362
edits
Modules avx512: Difference between revisions
Jump to navigation
Jump to search
no edit summary
No edit summary |
No edit summary |
||
| Line 40: | Line 40: | ||
| <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> | ||
|- | |- | ||
| 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> | ||
|- | |- | ||
| align="center" | [https://projects.coin-or.org/ADOL-C adol-c] | | align="center" | [https://projects.coin-or.org/ADOL-C adol-c] | ||
| Line 82: | Line 82: | ||
| align="center" | [http://ambermd.org/amber.html amber] | | align="center" | [http://ambermd.org/amber.html amber] | ||
| align="center" | chem | | align="center" | chem | ||
| align="center" | 20.9-20.15 | | align="center" | 22.5-23.5, 20.9-20.15, 20.12-20.15, 18.14-18.17 | ||
| <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: http://ambermd.org/amber.html URL: http://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, 23.5 | | align="center" | 20, 21, 22, 23, 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> | ||
|- | |- | ||
| Line 207: | Line 207: | ||
| 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, | | 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> | ||
|- | |- | ||
| Line 667: | Line 667: | ||
| 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> | ||
|- | |- | ||
| Line 777: | Line 777: | ||
| 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, 6.0.0.405, 6.1.0.357, 6.2.0.415 | | align="center" | 5.6, 6.0, 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> | ||
|- | |- | ||
| Line 1,437: | Line 1,437: | ||
| 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> | ||
|- | |- | ||
| Line 1,548: | Line 1,548: | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 3.3.2, 3.3.8 | | align="center" | 3.3.2, 3.3.8 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop Homepage: https://www.glfw.org URL: https://www.glfw.org<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm] | | align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm] | ||
| Line 1,582: | Line 1,582: | ||
| 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" | | | align="center" | 2024-08-20, 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> | ||
|- | |- | ||
| Line 1,657: | Line 1,657: | ||
| align="center" | [http://www.gromacs.org gromacs] | | align="center" | [http://www.gromacs.org gromacs] | ||
| 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, 2023.5, 2024.1 | | align="center" | 2016.6, 2020.4, 2020.6, 2021.2, 2021.4, 2021.6, 2022.2, 2022.3, 2023, 2023.2, 2023.3, 2023.5, 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> | ||
|- | |- | ||
| align="center" | [http://colvars.github.io/ gromacs-colvars] | | align="center" | [http://colvars.github.io/ gromacs-colvars] | ||
| Line 1,927: | Line 1,927: | ||
| 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" | 5.50-84.0, 5.64-96.0, 5.63-95.0, 5.53-87.0, 5.56-89.0, 5.55-88.0, 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> | ||
|- | |- | ||
| 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> | ||
|- | |- | ||
| Line 2,017: | Line 2,017: | ||
| align="center" | [http://openjdk.java.net java] | | align="center" | [http://openjdk.java.net java] | ||
| align="center" | tools | | align="center" | tools | ||
| align="center" | 1.8.0_292, 11.0.16_8, 1.8.0_192, 11.0.22, 13.0.2, 14.0.2, 17.0.2, 17.0.6, 21.0.1 | | align="center" | 1.8.0_292, 11.0.16_8, 1.8.0_192, 11.0.2, 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> | ||
|- | |- | ||
| Line 2,323: | Line 2,323: | ||
| 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> | ||
|- | |- | ||
| align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9] | | align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9] | ||
| Line 2,557: | Line 2,557: | ||
| 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" | R2021b, R2022b, R2020b, 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: 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> | ||
|- | |- | ||
| Line 2,702: | Line 2,702: | ||
| 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 2,998: | Line 2,998: | ||
| 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/3.8, python/3.9, python/3.10 Keyword:math<br /><br /><br /></div> | ||
|- | |- | ||
| align="center" | [https://nodejs.org nodejs] | | align="center" | [https://nodejs.org nodejs] | ||
| Line 3,197: | Line 3,197: | ||
| 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> | ||
|- | |- | ||
| Line 3,552: | Line 3,552: | ||
| 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" | 1.9b_6.21-x86_64, 2.00a5.8, 2.00-20231024-avx2, 2.00a3.6, 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> | ||
|- | |- | ||
| Line 3,815: | Line 3,815: | ||
| <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> | ||
|- | |- | ||
| 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> | ||
|- | |- | ||
| align="center" | [http://qwtpolar.sourceforge.net/ qwtpolar] | | align="center" | [http://qwtpolar.sourceforge.net/ qwtpolar] | ||
| Line 3,940: | Line 3,940: | ||
| <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> | ||
|- | |- | ||
| 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> | ||
|- | |- | ||
| align="center" | [https://repast.github.io/ repasthpc] | | align="center" | [https://repast.github.io/ repasthpc] | ||