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| align="center" | [https://github.com/beagle-dev/beagle-lib beagle-lib] | | align="center" | [https://github.com/beagle-dev/beagle-lib beagle-lib] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 2.1.2, 3.1.1, 3.1.2, 4.0.0 | | align="center" | 2.1.2, 3.1.1, 3.1.2, 4.0.0, 4.0.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib URL: https://github.com/beagle-dev/beagle-lib Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib URL: https://github.com/beagle-dev/beagle-lib Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | phys | | align="center" | phys | ||
| align="center" | 1.2.5 | | align="center" | 1.2.5 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. Homepage | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. Homepage: http://www.icams.de/content/departments/cmat/boltztrap/ Keyword:phys<br /><br /><br /></div> | ||
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| align="center" | [https://www.boost.org/ boost] | | align="center" | [https://www.boost.org/ boost] | ||
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| align="center" | [http://bio-bwa.sourceforge.net/ bwa] | | align="center" | [http://bio-bwa.sourceforge.net/ bwa] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 0.7.15, 0.7.17 | | align="center" | 0.7.15, 0.7.17, 0.7.18 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Homepage: http://bio-bwa.sourceforge.net/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Homepage: http://bio-bwa.sourceforge.net/ URL: http://bio-bwa.sourceforge.net/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://github.com/bwa-mem2/bwa-mem2 bwa-mem2] | | align="center" | [https://github.com/bwa-mem2/bwa-mem2 bwa-mem2] | ||
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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" | 5.3a, 5.4, 5.5, 5.6, 6.0.0.405, 6.1, 6.1.0.357 | | align="center" | 5.3a, 5.4, 5.5, 5.6, 6.0.0.405, 6.1, 6.1.0.357, 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/rrwick/Filtlong filtlong] | | align="center" | [https://github.com/rrwick/Filtlong filtlong] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 0.2.0 | | align="center" | 0.2.0, 0.2.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage: https://github.com/rrwick/Filtlong Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter Homepage: https://github.com/rrwick/Filtlong URL: https://github.com/rrwick/Filtlong Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html fineradstructure] | | align="center" | [http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html fineradstructure] | ||
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| align="center" | [https://github.com/freebayes/freebayes freebayes] | | align="center" | [https://github.com/freebayes/freebayes freebayes] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.1.0, 1.2.0, 1.3.6 | | align="center" | 1.1.0, 1.2.0, 1.3.6, 1.3.7 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Homepage: https://github.com/freebayes/freebayes URL: https://github.com/freebayes/freebayes Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Homepage: https://github.com/freebayes/freebayes URL: https://github.com/freebayes/freebayes Keyword:bio<br /><br /><br /></div> | ||
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| 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> | ||
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| align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm] | | align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm] | ||
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| align="center" | bio | | align="center" | bio | ||
| align="center" | 3.23, 4.0.0beta2 | | align="center" | 3.23, 4.0.0beta2 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://graal.ens-lyon.fr/MUMPS/ mumps-metis] | | align="center" | [https://graal.ens-lyon.fr/MUMPS/ mumps-metis] | ||
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| align="center" | [https://podman.io podman] | | align="center" | [https://podman.io podman] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 4.1.1, 4.5.0 | | align="center" | 4.1.1, 4.5.0, 4.9.5 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Podman is a daemonless container engine for developing, managing, and running OCI Containers on your Linux System. Homepage: https://podman.io URL: https://podman.io<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Podman is a daemonless container engine for developing, managing, and running OCI Containers on your Linux System. Homepage: https://podman.io URL: https://podman.io<br /><br /><br /></div> | ||
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| align="center" | [https://repast.github.io/ repasthpc] | | align="center" | [https://repast.github.io/ repasthpc] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | | | align="center" | 2.2.0, 2.3.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. Homepage: https://repast.github.io/ URL: https://repast.github.io/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. Homepage: https://repast.github.io/ URL: https://repast.github.io/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | - | | align="center" | - | ||
| align="center" | 6.0.1.5, 8.6.1.6 | | align="center" | 6.0.1.5, 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/3.10, 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/3.8, python/3.9, 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] | ||