Paket: parsnp (2.1.3+dfsg-1)

[ Källkod: 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.

Andra paket besläktade med 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 (>= 2.38)

  GNU C-bibliotek: Delade bibliotek
  också ett virtuellt paket som tillhandahålls av libc6-udeb

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

  GCC stödbibliotek

  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 standardbibliotek v3 för C++

• 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

  Python library for numerical computations (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)

Hämta parsnp

Hämtningar för alla tillgängliga arkitekturer

Arkitektur	Paketstorlek	Installerad storlek	Filer
amd64	209,3 kbyte	1.959,0 kbyte	[filförteckning]
arm64	196,0 kbyte	1.947,0 kbyte	[filförteckning]
armel	190,5 kbyte	1.946,0 kbyte	[filförteckning]
armhf	187,1 kbyte	1.882,0 kbyte	[filförteckning]
i386	205,7 kbyte	1.950,0 kbyte	[filförteckning]
mips64el	205,3 kbyte	2.020,0 kbyte	[filförteckning]
ppc64el	216,2 kbyte	2.011,0 kbyte	[filförteckning]
riscv64	214,3 kbyte	1.871,0 kbyte	[filförteckning]
s390x	188,2 kbyte	1.951,0 kbyte	[filförteckning]