Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates' recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a…

• WT
  Wellcome Trust

  Award: 098051
• MR
  Medical Research Council

  Awards: MR/K010174/1, MR/L015080/1