Paket: parsnp (2.0.6+dfsg-1)

[ Kaynak: 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.

parsnp ile İlgili Diğer Paketler

• 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
  ayrıca şunun tarafından sağlanan bir sanal paket libc6-udeb

• dep: libgcc-s1 (>= 3.0) [armel, armhf, riscv64 değil]

  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)

parsnp indir

Tüm mevcut mimariler için indir

Mimari	Paket Boyutu	Kurulu Boyut	Dosyalar
amd64	208,2 kB	1.958,0 kB	[dosya listesi]
arm64	194,8 kB	1.946,0 kB	[dosya listesi]
armel	190,1 kB	1.905,0 kB	[dosya listesi]
armhf	186,1 kB	1.829,0 kB	[dosya listesi]
i386	205,1 kB	1.949,0 kB	[dosya listesi]
mips64el	203,4 kB	2.019,0 kB	[dosya listesi]
ppc64el	215,4 kB	2.010,0 kB	[dosya listesi]
riscv64	213,9 kB	1.870,0 kB	[dosya listesi]
s390x	187,8 kB	1.950,0 kB	[dosya listesi]