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PLoS Comput Biol. 2015 Feb 12;11(2):e1004041. doi: 10.1371/journal.pcbi.1004041. eCollection 2015 Feb.

ClonalFrameML: efficient inference of recombination in whole bacterial genomes.

Author information

1
Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom.
2
Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom; Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.

Abstract

Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/.

PMID:
25675341
PMCID:
PMC4326465
DOI:
10.1371/journal.pcbi.1004041
[Indexed for MEDLINE]
Free PMC Article

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