[ Source: parsnp ]
Package: parsnp (1.5.4+dfsg-1)
Links for parsnp
Debian Resources:
Download Source Package parsnp:
Maintainers:
External Resources:
- Homepage [harvest.readthedocs.org]
Similar packages:
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.
Other Packages Related to parsnp
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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 (>= 2.27)
- GNU C Library: Shared libraries
also a virtual package provided by libc6-udeb
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- dep: libgcc-s1 (>= 3.0) [not armel, armhf]
- GCC support library
- dep: libgcc-s1 (>= 3.5) [armel, armhf]
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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 (>= 5.2)
- 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-numpy
- Fast array facility to the Python 3 language
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- dep: raxml
- Randomized Axelerated Maximum Likelihood of phylogenetic trees
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- rec: python3-dendropy
- DendroPy Phylogenetic Computing Library (Python 3)
Download parsnp
| Architecture | Package Size | Installed Size | Files |
|---|---|---|---|
| amd64 | 185.2 kB | 1,881.0 kB | [list of files] |
| arm64 | 174.9 kB | 1,837.0 kB | [list of files] |
| armel | 167.3 kB | 1,836.0 kB | [list of files] |
| armhf | 164.4 kB | 1,760.0 kB | [list of files] |
| i386 | 188.3 kB | 1,900.0 kB | [list of files] |
| mips64el | 185.0 kB | 1,927.0 kB | [list of files] |
| mipsel | 187.4 kB | 1,925.0 kB | [list of files] |
| ppc64el | 197.4 kB | 1,945.0 kB | [list of files] |
| s390x | 169.9 kB | 1,885.0 kB | [list of files] |