ClonalFrame: inference of bacterial microevolution using multilocus sequence data


This is the homepage of ClonalFrame, 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.

The methods used in ClonalFrame are presented in the paper "Inference of bacterial microevolution using multilocus sequence data" by Didelot and Falush (2007), which is the appropriate citation for this program.

New in 2015: if you want to use ClonalFrame to infer recombination in large whole genome datasets, see ClonalFrameML


Before you start using ClonalFrame, it would be very helpful if you could register by clicking here. This is optional, however this information is useful for us in planning possible future upgrades of the software. Registered users will also be kept informed of updates via email Thank you.

Getting help

Click here to download the ClonalFrame user guide in PDF format. It is also included in each downloadable package.
The paper describing the methods is also available: Didelot and Falush (2007)
If you have a question or a problem that is not discussed in the user guide, please get in touch.


Version 1.2 (current release):

Version 1.1:

Version 1.0:


xmfa2struct is a program written in C which converts files in eXtended Multi-Fasta format (XMFA, the input format of ClonalFrame) into the input file format of Structure.