ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
Imperial College London · Centre for Human Genetics · +2 more institutions
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…
Citation impact
- FWCI
- 31.32
- Percentile
- 100%
- References
- 81
Authors
2Topics & keywords
- Recombination
- Genome
- Inference
- Biology
- Phylogenetic tree
- Computational biology
- Evolutionary biology
- Phylogenetics
Funding
- WTWellcome TrustAwards: 101237/Z/13/Z, 087646/Z/08/Z, 101237
- UKUnited Kingdom Clinical Research Collaboration
- NINational Institute for Health Research Health Protection Research Unit
- NINational Institute for Health and Care ResearchAward: G0800778
- RSRoyal SocietyAward: 101237/Z/13/Z
- DFDirectorate for Biological Sciences
- MRMedical Research CouncilAwards: MR/K010174/1, G0800778
- BABiotechnology and Biological Sciences Research CouncilAward: BB/L023458/1