Pakket: parsnp (2.0.6+dfsg-1 en anderen)

[ 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) [niet alpha, ia64, sh4]

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

  dep: libc6 (>= 2.40) [sh4]

• dep: libc6.1 (>= 2.37) [ia64]

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6.1-udeb

  dep: libc6.1 (>= 2.38) [alpha]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, i386, mips64el, ppc64, ppc64el, s390x, x32]

  GCC support bibliotheek

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sh4, sparc64]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support bibliotheek

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support bibliotheek

• dep: libgomp1 (>= 6)

  GCC OpenMP (GOMP) support library

• dep: libmuscle1 (>= 3.7+4565)

  multiple alignment library for protein sequences

• dep: libstdc++6 (>= 13.1) [ia64, m68k]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 14) [niet ia64, m68k]

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• 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 downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Versie	Pakketgrootte	Geïnstalleerde grootte	Bestanden
alpha (unofficial port)	2.0.6+dfsg-1	210,3 kB	2.011,0 kB	[overzicht]
amd64	2.0.6+dfsg-1	208,2 kB	1.958,0 kB	[overzicht]
arm64	2.0.6+dfsg-1	194,8 kB	1.946,0 kB	[overzicht]
armel	2.0.6+dfsg-1	190,1 kB	1.905,0 kB	[overzicht]
armhf	2.0.6+dfsg-1	186,1 kB	1.829,0 kB	[overzicht]
hppa (unofficial port)	2.0.6+dfsg-1	202,6 kB	1.915,0 kB	[overzicht]
i386	2.0.6+dfsg-1	205,1 kB	1.949,0 kB	[overzicht]
ia64 (unofficial port)	2.0.5+dfsg-1	256,9 kB	2.246,0 kB	[overzicht]
m68k (unofficial port)	2.0.6+dfsg-1	190,5 kB	1.929,0 kB	[overzicht]
mips64el	2.0.6+dfsg-1	203,4 kB	2.019,0 kB	[overzicht]
ppc64 (unofficial port)	2.0.6+dfsg-1	212,3 kB	2.010,0 kB	[overzicht]
ppc64el	2.0.6+dfsg-1	215,4 kB	2.010,0 kB	[overzicht]
riscv64	2.0.6+dfsg-1	213,9 kB	1.870,0 kB	[overzicht]
s390x	2.0.6+dfsg-1	187,8 kB	1.950,0 kB	[overzicht]
sh4 (unofficial port)	2.0.6+dfsg-1	235,9 kB	1.946,0 kB	[overzicht]
sparc64 (unofficial port)	2.0.6+dfsg-1	186,3 kB	2.654,0 kB	[overzicht]
x32 (unofficial port)	2.0.6+dfsg-1	209,4 kB	1.941,0 kB	[overzicht]