Package: gubbins (3.4-1)

[ Source: 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.

Other Packages Related to gubbins

• dep: libc6 (>= 2.34)

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

  better multiprocessing and multithreading in Python

• dep: python3-numpy

  Fast array facility to the Python language (Python 3)

• dep: python3-scipy

  scientific tools for Python 3

• dep: raxml

  Randomized Axelerated Maximum Likelihood of phylogenetic trees

• dep: zlib1g (>= 1:1.1.4)

  compression library - runtime

• 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

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