[ Bron: parsnp ]
Pakket: parsnp (2.0.5+dfsg-1)
Verwijzigingen voor parsnp
Debian bronnen:
Het bronpakket parsnp downloaden:
Beheerders:
- Debian Med Packaging Team (QA-pagina, Mailarchief)
- Andreas Tille (QA-pagina)
- Étienne Mollier (QA-pagina)
Externe bronnen:
- Homepage [harvest.readthedocs.org]
Vergelijkbare pakketten:
rapid core genome multi-alignment
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
Andere aan parsnp gerelateerde pakketten
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- dep: fasttree
- phylogenetic trees from alignments of nucleotide or protein sequences
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- dep: harvest-tools
- archiving and postprocessing for reference-compressed genomic multi-alignments
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- dep: libc6 (>= 2.34)
- GNU C Bibliotheek: Gedeelde bibliotheken
Ook een virtueel pakket geboden door: libc6-udeb
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- dep: libgcc-s1 (>= 3.0)
- GCC support bibliotheek
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- dep: libgomp1 (>= 6)
- GCC OpenMP (GOMP) support library
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- dep: libmuscle1 (>= 3.7+4565)
- multiple alignment library for protein sequences
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- dep: libstdc++6 (>= 13.1)
- GNU Standard C++ Library v3
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- dep: mummer
- Efficient sequence alignment of full genomes
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- dep: phipack
- PHI test and other tests of recombination
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- dep: python3
- interactive high-level object-oriented language (default python3 version)
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- dep: python3-biopython
- Python3 library for bioinformatics
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- dep: python3-numpy
- Fast array facility to the Python language (Python 3)
-
- dep: python3-pyspoa
- Python bindings to spoa
-
- dep: python3-tqdm
- fast, extensible progress bar for Python 3 and CLI tool
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- dep: raxml
- Randomized Axelerated Maximum Likelihood of phylogenetic trees
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- dep: time
- GNU time program for measuring CPU resource usage
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- rec: python3-dendropy
- DendroPy Phylogenetic Computing Library (Python 3)