ClonalFrame 1.2 / ClonalFrameML 1.0 – Inference of Bacterial Microevolution using Multilocus Sequence data

ClonalFrame 1.2 / ClonalFrameML 1.0


ClonalFrame is a computer package for the inference of bacterial microevolution using multilocus sequence data.In a nutshell, ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, we recommend using Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes.


Xavier Didelot and Daniel Wilson



  • Linux / Windows / MacOsX


 ClonalFrame , ClonalFrameML



ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Didelot X, Wilson DJ.
PLoS Comput Biol. 2015 Feb 12;11(2):e1004041. doi: 10.1371/journal.pcbi.1004041.

Didelot and Falush (2007)
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Genetics March 2007 vol. 175 no. 3 1251-1266