ClonalFrameML: efficient inference of recombination in whole bacterial genomes

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


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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Clostridioides difficile / classification
  • Clostridioides difficile / genetics
  • Computer Simulation
  • Databases, Genetic
  • Evolution, Molecular
  • Genome, Bacterial / genetics*
  • Genomics / methods*
  • Phylogeny
  • Recombination, Genetic / genetics*
  • Sequence Analysis, DNA
  • Software*
  • Staphylococcus aureus / classification
  • Staphylococcus aureus / genetics