Package: parsnp (2.0.4+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 (>= 2.34)

  GNU Biblioteca C: Bibliotecas compartilhadas
  also a virtual package provided by libc6-udeb

• dep: libgcc-s1 (>= 3.5)

  Biblioteca de suporte GCC

• dep: libgomp1 (>= 6)

  biblioteca de suporte ao GCC OpenMP (GOMP)

• dep: libmuscle1 (>= 3.7+4565)

  multiple alignment library for protein sequences

• dep: libstdc++6 (>= 13.1)

  Biblioteca C++ padrão da GNU v3

• dep: mummer

  alinhamento eficiente de seqüência para genomas completos

• dep: phipack

  PHI test and other tests of recombination

• dep: python3

  linguagem orientada a objetos de alto nível e interativa (versão python3 padrão)

• 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

  programa "time" do GNU para medição do uso de recursos da CPU

• rec: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

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Architecture	Package Size	Installed Size	Files
armhf	181.7 kB	1,824.0 kB	[list of files]