Pakket: parsnp (2.1.3+dfsg-1)

[ Bron: 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.

Andere aan parsnp gerelateerde pakketten

• 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 Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6-udeb

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

  GCC support bibliotheek

  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

  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)

parsnp downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Pakketgrootte	Geïnstalleerde grootte	Bestanden
amd64	209,3 kB	1.959,0 kB	[overzicht]
arm64	196,0 kB	1.947,0 kB	[overzicht]
armel	190,5 kB	1.946,0 kB	[overzicht]
armhf	187,1 kB	1.882,0 kB	[overzicht]
i386	205,7 kB	1.950,0 kB	[overzicht]
mips64el	205,3 kB	2.020,0 kB	[overzicht]
ppc64el	216,2 kB	2.011,0 kB	[overzicht]
riscv64	214,3 kB	1.871,0 kB	[overzicht]
s390x	188,2 kB	1.951,0 kB	[overzicht]