Pakket: gubbins (3.4-1 en anderen)

[ Bron: gubbins  ]

phylogenetic analysis of genome sequences

Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.

Andere aan gubbins gerelateerde pakketten

• dep: fasttree [niet amd64, i386]

  phylogenetic trees from alignments of nucleotide or protein sequences

• dep: libc6 (>= 2.27) [riscv64]

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

  dep: libc6 (>= 2.29) [m68k, ppc64]

  dep: libc6 (>= 2.34) [amd64, i386]

• dep: libc6.1 (>= 2.29) [alpha]

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

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-biopython

  Python3 library for bioinformatics

• dep: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

• dep: python3-multiprocess [amd64, i386]

  better multiprocessing and multithreading in Python

• dep: python3-nose [niet amd64, i386]

  test discovery and running for Python3 unittest

• dep: python3-numpy [amd64, i386]

  Fast array facility to the Python language (Python 3)

• dep: python3-reportlab [niet amd64, i386]

  ReportLab library to create PDF documents using Python3

• dep: python3-scipy [amd64, i386]

  scientific tools for Python 3

• dep: raxml

  Randomized Axelerated Maximum Likelihood of phylogenetic trees

• dep: zlib1g (>= 1:1.1.4)

  compressiebibliotheek - programma's

• rec: fasttree

  phylogenetic trees from alignments of nucleotide or protein sequences

• rec: iqtree

  efficient phylogenetic software by maximum likelihood

• sug: r-base-core

  GNU R core of statistical computation and graphics system

gubbins downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Versie	Pakketgrootte	Geïnstalleerde grootte	Bestanden
alpha (unofficial port)	2.3.5-1	53,5 kB	201,0 kB	[overzicht]
amd64	3.4-1	92,8 kB	482,0 kB	[overzicht]
i386	3.4-1	93,6 kB	485,0 kB	[overzicht]
m68k (unofficial port)	2.3.5-1	46,0 kB	174,0 kB	[overzicht]
ppc64 (unofficial port)	2.3.5-1	55,4 kB	312,0 kB	[overzicht]
riscv64 (unofficial port)	2.3.5-1	48,1 kB	168,0 kB	[overzicht]