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Package: parsnp (1.6.2+dfsg-1)

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

  • depends
  • recommends
  • suggests
  • 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 (>= 2.34)
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libgcc-s1 (>= 3.3.1) [not armhf]
    GCC support library
    dep: libgcc-s1 (>= 3.5) [armhf]
  • dep: libgomp1 (>= 6)
    GCC OpenMP (GOMP) support library
  • dep: libmuscle1 (>= 3.7+4565)
    multiple alignment library for protein sequences
  • dep: libstdc++6 (>= 11)
    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-numpy
    Fast array facility to the Python 3 language
  • dep: raxml
    Randomized Axelerated Maximum Likelihood of phylogenetic trees

Download parsnp

Download for all available architectures
Architecture Package Size Installed Size Files
amd64 184.0 kB1822 kB [list of files]
arm64 183.2 kB1782 kB [list of files]
armhf 186.9 kB1757 kB [list of files]
ppc64el 208.2 kB1882 kB [list of files]