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[ Paquet source : parsnp  ]

Paquet : parsnp (1.2.1+dfsg-1build1)

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.

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  • dep: fasttree
    phylogenetic trees from alignments of nucleotide or protein sequences
  • dep: libc6 (>= 2.27)
    GNU C Library: Shared libraries
    un paquet virtuel est également fourni par libc6-udeb
  • dep: libgcc-s1 (>= 3.0) [amd64]
    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 (>= 5.2)
    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

Télécharger parsnp

Télécharger pour toutes les architectures proposées
Architecture Taille du paquet Espace occupé une fois installé Fichiers
amd64 190,4 ko1987 ko [liste des fichiers]
armhf 164,9 ko1846 ko [liste des fichiers]