Bug#764232: ITP: gubbins -- 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.

[Jorge Soares <j.s.soares@gmail.com>]

Package: wnpp
Severity: wishlist
Owner: Jorge Soares <j.s.soares@gmail.com>

* Package name    : gubbins
  Version         : 0.6
  Upstream Author : Andrew Page <ap13@sanger.ac.uk> 
* URL             : https://github.com/sanger-pathogens/gubbins
* License         : GPL2
  Programming Lang: C, Python
  Description     : 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.

Since the introduction of high-throughput, second-generation DNA sequencing technologies,
there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics.
Although many phylogenetic techniques are scalable to hundreds of bacterial genomes,
methods which have been used for mitigating the effect of mechanisms of horizontal sequence
transfer on phylogenetic reconstructions cannot cope with these new datasets.
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.