RT Journal Article SR Electronic T1 Analysis of recent and ancestral recombination reveals high-resolution population structure in Streptococcus pneumoniae JF bioRxiv FD Cold Spring Harbor Laboratory SP 059642 DO 10.1101/059642 A1 Rafal Mostowy A1 Nicholas J. Croucher A1 Cheryl P. Andam A1 Jukka Corander A1 William P. Hanage A1 Pekka Marttinen YR 2016 UL http://biorxiv.org/content/early/2016/06/18/059642.abstract AB Bacterial population genomic analyses rely on identification of genetic recombinations, but growing databases represent a challenge for computational methods to detect these recombinations and interpret sequence ancestry. We introduce a novel algorithm called fastGEAR which identifies major lineages in diverse microbial alignments and recombinations between them. The algorithm can detect not only recent recombinations, but also the ancestral ones affecting entire lineages. Using simulated data, fastGEAR demonstrates outstanding power to detect ancestral recombination events compared to other state-of-the-art methods. The utility is further demonstrated by analysing 616 whole genomes of Streptococcus pneumoniae, providing novel insights into the evolution of recom-binogenic bacteria.