ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

• DOI: 10.1371/journal.pcbi.1004041
• Publication Date: 2015-02-12T18:49:28Z
• Authors: Xavier Didelot; Daniel J. Wilson
• Keywords: Recombination, Genetic; Staphylococcus aureus; 0303 health sciences; QH301-705.5; Clostridioides difficile; Genomics; Sequence Analysis, DNA; 3. Good health; Evolution, Molecular; 03 medical and health sciences; Databases, Genetic; Computer Simulation; Biology (General); Genome, Bacterial; Phylogeny; Software; Research Article

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