Paketti: parsnp (1.5.4+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.

Muut pakettiin parsnp liittyvät paketit

• 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 (>= 2.27)

  GNU-C-kirjasto: jaetut kirjastot
  myös näennäispaketti, jonka toteuttaa libc6-udeb

• dep: libgcc-s1 (>= 3.0) [ei armel, armhf]

  GCC:n apukirjasto

  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 (>= 5.2)

  GNU standardi C++ -kirjasto, versio 3

• 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

• rec: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

Imuroi parsnp

Imurointi kaikille saataville arkkitehtuureille

Arkkitehtuuri	Paketin koko	Koko asennettuna	Tiedostot
amd64	185.2 kt	1,881.0 kt	[tiedostoluettelo]
arm64	174.9 kt	1,837.0 kt	[tiedostoluettelo]
armel	167.3 kt	1,836.0 kt	[tiedostoluettelo]
armhf	164.4 kt	1,760.0 kt	[tiedostoluettelo]
i386	188.3 kt	1,900.0 kt	[tiedostoluettelo]
mips64el	185.0 kt	1,927.0 kt	[tiedostoluettelo]
mipsel	187.4 kt	1,925.0 kt	[tiedostoluettelo]
ppc64el	197.4 kt	1,945.0 kt	[tiedostoluettelo]
s390x	169.9 kt	1,885.0 kt	[tiedostoluettelo]