TY - JOUR T1 - Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments A1 - Westesson, Oscar A1 - Holmes, Ian Y1 - 2009/03/20 N2 - Author Summary In viral and bacterial pathogens, recombination has the ability to combine fitness-enhancing mutations. Accurate characterization of recombinant breakpoints in newly sequenced strains can provide information about the role of this process in evolution, for example, in immune evasion. Of particular interest are situations of an admixture of pathogen subspecies, recombination between whose genomes may change the apparent phylogenetic tree topology in different regions of a multiple-genome alignment. We describe an algorithm that can pinpoint recombination breakpoints to greater accuracy than previous methods, allowing detection of both short recombinant regions and long-range multiple crossovers. The algorithm is appropriate for the analysis of fast-evolving pathogen sequences where repeated substitutions may be observed at a single site in a multiple alignment (violating the “infinite sites” assumption inherent to some other breakpoint-detection algorithms). Simulations demonstrate the practicality of our implementation for alignments of longer sequences and more taxa than previous methods. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 5 IS - 3 UR - https://doi.org/10.1371/journal.pcbi.1000318 SP - e1000318 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000318 ER -