The variety of evolutionary mechanisms by which bacteria evolve can pose problems when attempting to infer relationships between strains. Clonal frame is an approach developed by Didelot and Falush for MLST data (2007), which does infer the clonal relationship of bacteria by accounting for not only point mutations but also recombination events. The model estimates the extent of the clonal frame for each branch of the genealogy, which is the subset of the genome that has not undergone recombination.

This method can be used to decide whether a subset of isolates share common ancestry, to estimate the age of the common ancestor and hence to address a variety of epidemiological and ecological questions that hinge on the pattern of bacterial spread. However, be aware that since the key assumption of the model concerns recombination, and currently it does not model the origin of genetic imports, the model tends to underestimate the number of recombination compared to mutation events and can infer incorrect subdivisions, particularly if recombination is relatively frequent compared to mutation.

The algorithms have been implemented in a computer software package which is freely available at the webpage of the Department of Statistics of the University of Warwick.

Reference:
Didelot, X. and Falush, D. (2007) Inference of Bacterial Microevolution using Multilocus Sequence Data. Genetics 175, 1251-1266.