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| align="center" | 3.1.0 | | align="center" | 3.1.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open-source library for mathematical programming. Homepage: https://github.com/ampl/mp URL: https://github.com/ampl/mp<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: An open-source library for mathematical programming. Homepage: https://github.com/ampl/mp URL: https://github.com/ampl/mp<br /><br /><br /></div> | ||
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| align="center" | [https://megares.meglab.org/amrplusplus/latest/html/v2 amrplusplus] | |||
| align="center" | - | |||
| align="center" | 2.0-20200114 | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragments of DNA, and count them. It also provides a count of the polymorphisms that occur in each DNA fragment with respect to the reference database. Homepage: https://megares.meglab.org/amrplusplus/latest/html/v2 URL: https://megares.meglab.org/amrplusplus/latest/html/v2<br /><br /><br /></div> | |||
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| align="center" | [http://www.popgen.dk/angsd angsd] | | align="center" | [http://www.popgen.dk/angsd angsd] | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [ | | align="center" | [https://ccb.jhu.edu/software/bracken/ bracken] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 2.5, 2.6.0 | | align="center" | 2.5, 2.6.0, 2.7 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bracken is a | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. Homepage: https://ccb.jhu.edu/software/bracken/ URL: https://ccb.jhu.edu/software/bracken/<br /><br /><br /></div> | ||
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| align="center" | [http://gmt.genome.wustl.edu/packages/breakdancer breakdancer] | | align="center" | [http://gmt.genome.wustl.edu/packages/breakdancer breakdancer] | ||
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| align="center" | [https://www.nextflow.io/ nextflow] | | align="center" | [https://www.nextflow.io/ nextflow] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 19.04.0, 19.10.0, 20.04.1, 20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6 | | align="center" | 19.04.0, 19.10.0, 20.04.1, 20.10.0, 21.04.3, 21.10.3, 22.04.3, 22.10.6, 22.10.8 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Homepage: https://www.nextflow.io/ URL: https://www.nextflow.io/<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Homepage: https://www.nextflow.io/ URL: https://www.nextflow.io/<br /><br /><br /></div> | ||
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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. Homepage: https://github.com/Illumina/strelka URL: https://github.com/Illumina/strelka<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. Homepage: https://github.com/Illumina/strelka URL: https://github.com/Illumina/strelka<br /><br /><br /></div> | ||
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| align="center" | [ | | align="center" | [https://ccb.jhu.edu/software/stringtie/ stringtie] | ||
| align="center" | bio | | align="center" | bio | ||
| align="center" | 1.3.4d, 2.0, 2.1.0, 2.1.3, 2.1.5 | | align="center" | 1.3.4d, 2.0, 2.1.0, 2.1.3, 2.1.5 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts Homepage: https://ccb.jhu.edu/software/stringtie/ URL: https://ccb.jhu.edu/software/stringtie/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [http://web.stanford.edu/group/pritchardlab/software/ structure] | | align="center" | [http://web.stanford.edu/group/pritchardlab/software/ structure] | ||
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| align="center" | chem | | align="center" | chem | ||
| align="center" | 6.3.0, 6.3.3, 6.4.0, 6.4.1, 6.5.0, 6.5.1 | | align="center" | 6.3.0, 6.3.3, 6.4.0, 6.4.1, 6.5.0, 6.5.1 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtb - Extended tight-binding semi-empirical quantum mechanics Homepage: https://github.com/grimme-lab/xtb URL: https://github.com/grimme-lab/xtb Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: ase-3.22.1, Pint-0.19.2, pydantic-1.9.1, qcelemental-0.24.0, xtb-6.5. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: xtb - Extended tight-binding semi-empirical quantum mechanics Homepage: https://github.com/grimme-lab/xtb URL: https://github.com/grimme-lab/xtb Compatible modules: python/3.8, python/3.9, python/3.10 Extensions: ase-3.22.1, Pint-0.19.2, pydantic-1.9.1, qcelemental-0.24.0, xtb-6.5.1 Keyword:chem<br /><br /><br /></div> | ||
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| align="center" | [https://github.com/xtensor-stack/xtensor xtensor] | | align="center" | [https://github.com/xtensor-stack/xtensor xtensor] | ||