Package: parsnp (2.0.6+dfsg-1)

[ Source: parsnp  ]

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

• dep: fasttree

  phylogenetic trees from alignments of nucleotide or protein sequences

• dep: harvest-tools

  archiving and postprocessing for reference-compressed genomic multi-alignments

• dep: libc6 (>= 2.38)

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libgcc-s1 (>= 3.0) [not armel, armhf, riscv64]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [riscv64]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

• dep: libgomp1 (>= 6)

  GCC OpenMP (GOMP) support library

• dep: libmuscle1 (>= 3.7+4565)

  multiple alignment library for protein sequences

• dep: libstdc++6 (>= 14)

  GNU Standard C++ Library v3

• dep: mummer

  Efficient sequence alignment of full genomes

• dep: phipack

  PHI test and other tests of recombination

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-biopython

  Python3 library for bioinformatics

• 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

• dep: raxml

  Randomized Axelerated Maximum Likelihood of phylogenetic trees

• dep: time

  GNU time program for measuring CPU resource usage

• rec: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

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Architecture	Package Size	Installed Size	Files
amd64	208.2 kB	1,958.0 kB	[list of files]
arm64	194.8 kB	1,946.0 kB	[list of files]
armel	190.1 kB	1,905.0 kB	[list of files]
armhf	186.1 kB	1,829.0 kB	[list of files]
i386	205.1 kB	1,949.0 kB	[list of files]
mips64el	203.4 kB	2,019.0 kB	[list of files]
ppc64el	215.4 kB	2,010.0 kB	[list of files]
riscv64	213.9 kB	1,870.0 kB	[list of files]
s390x	187.8 kB	1,950.0 kB	[list of files]