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| align="center" | [https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus amrfinderplus] | | align="center" | [https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus amrfinderplus] | ||
| align="center" | - | | align="center" | - | ||
| align="center" | 3.11.18 | | align="center" | 3.11.18, 3.11.26 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. Homepage: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus URL: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This software and the accompanying database identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. Homepage: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus URL: https://github.com/ncbi/amr/wiki/Running-AMRFinderPlus<br /><br /><br /></div> | ||
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| align="center" | 2.1.1, 2.10.7, 2.17.3, 2.18.9, 2.20.6, 2.23.2, 2.23.3, 2.26.3 | | align="center" | 2.1.1, 2.10.7, 2.17.3, 2.18.9, 2.20.6, 2.23.2, 2.23.3, 2.26.3 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ URL: http://broadinstitute.github.io/picard/ Keyword:bio<br /><br /><br /></div> | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. Homepage: http://broadinstitute.github.io/picard/ URL: http://broadinstitute.github.io/picard/ Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://www.drive5.com/pilercr/ pilercr] | |||
| align="center" | - | |||
| align="center" | 1.06 | |||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: PILERCR is public domain software for finding CRISPR repeats. It is part of the PILER family of repeat analysis tools. Homepage: https://www.drive5.com/pilercr/ URL: https://www.drive5.com/pilercr/<br /><br /><br /></div> | |||
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| align="center" | [https://github.com/broadinstitute/pilon pilon] | | align="center" | [https://github.com/broadinstitute/pilon pilon] | ||
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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" | 2.2.0, 2.3.0 | | align="center" | 2.0, 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" | bio | | align="center" | bio | ||
| align="center" | 3.0.2, 3.2.0, 3.2.1, 3.2.2, 4.0.0 | | align="center" | 3.0.2, 3.2.0, 3.2.1, 3.2.2, 4.0.0 | ||
| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ URL: https://trinotate.github.io/ Extensions: CGI-4. | | <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Homepage: https://trinotate.github.io/ URL: https://trinotate.github.io/ Extensions: CGI-4.57, Text::NSP-1.31 Keyword:bio<br /><br /><br /></div> | ||
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| align="center" | [https://triqs.github.io/triqs triqs] | | align="center" | [https://triqs.github.io/triqs triqs] | ||