Package: gubbins (2.3.4-1)

[ 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: fasttree

  phylogenetic trees from alignments of nucleotide or protein sequences

• dep: libc6 (>= 2.4)

  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

  Python library for bioinformatics (implemented in Python 3)

• dep: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

• dep: python3-nose

  test discovery and running for Python3 unittest

• dep: python3-reportlab

  ReportLab library to create PDF documents using Python3

• dep: raxml (>= 8)

  Randomized Axelerated Maximum Likelihood of phylogenetic trees

• dep: zlib1g (>= 1:1.1.4)

  compression library - runtime

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