Package: parsnp (2.1.3+dfsg-1 and others)

[ 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.

Other Packages Related to 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) [not alpha, ia64, loong64, sh4]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.40) [loong64, sh4]

• dep: libc6.1 (>= 2.37) [ia64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

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

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, i386, loong64, mips64el, ppc64, ppc64el, s390x, x32]

  GCC support library

  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 library

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC support library

• 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) [not 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

  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)

Download parsnp

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.1.3+dfsg-1	210.7 kB	2,012.0 kB	[list of files]
amd64	2.1.3+dfsg-1	209.3 kB	1,959.0 kB	[list of files]
arm64	2.1.3+dfsg-1	196.0 kB	1,947.0 kB	[list of files]
armel	2.1.3+dfsg-1	190.5 kB	1,946.0 kB	[list of files]
armhf	2.1.3+dfsg-1	187.1 kB	1,882.0 kB	[list of files]
hppa (unofficial port)	2.1.3+dfsg-1	203.5 kB	1,916.0 kB	[list of files]
i386	2.1.3+dfsg-1	205.7 kB	1,950.0 kB	[list of files]
ia64 (unofficial port)	2.0.5+dfsg-1	256.9 kB	2,246.0 kB	[list of files]
loong64 (unofficial port)	2.1.3+dfsg-1	203.3 kB	1,947.0 kB	[list of files]
m68k (unofficial port)	2.1.3+dfsg-1	191.4 kB	1,930.0 kB	[list of files]
mips64el	2.1.3+dfsg-1	205.3 kB	2,020.0 kB	[list of files]
ppc64 (unofficial port)	2.1.3+dfsg-1	212.8 kB	2,011.0 kB	[list of files]
ppc64el	2.1.3+dfsg-1	216.2 kB	2,011.0 kB	[list of files]
riscv64	2.1.3+dfsg-1	214.3 kB	1,871.0 kB	[list of files]
s390x	2.1.3+dfsg-1	188.2 kB	1,951.0 kB	[list of files]
sh4 (unofficial port)	2.1.3+dfsg-1	236.4 kB	1,947.0 kB	[list of files]
sparc64 (unofficial port)	2.1.3+dfsg-1	186.5 kB	2,655.0 kB	[list of files]
x32 (unofficial port)	2.1.3+dfsg-1	210.0 kB	1,942.0 kB	[list of files]