Paket: parsnp (1.5.4+dfsg-1)

[ Quellcode: 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 Pakete mit Bezug zu 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 (>= 2.27)

  GNU-C-Bibliothek: Laufzeitbibliotheken
  auch ein virtuelles Paket, bereitgestellt durch libc6-udeb

• dep: libgcc-s1 (>= 3.0)

  GCC Support-Bibliothek

• dep: libgomp1 (>= 6)

  Unterstützungsbibliothek für GCC OpenMP (GOMP)

• dep: libmuscle1 (>= 3.7+4565)

  multiple alignment library for protein sequences

• dep: libstdc++6 (>= 5.2)

  GNU-Implementierung der Standard-C++-Bibliothek (Version 3)

• dep: mummer

  Effizientes Sequenzalignment vollständiger Genome

• dep: phipack

  PHI test and other tests of recombination

• dep: python3

  Interaktive objektorientierte Hochsprache (Python3-Standardversion)

• dep: python3-numpy

  Schnelle Array-Einrichtung für die Sprache Python 3

• dep: raxml

  Randomized Axelerated Maximum Likelihood of phylogenetic trees

• rec: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

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Architektur	Paketgröße	Größe (installiert)	Dateien
i386	188,3 kB	1.900,0 kB	[Liste der Dateien]