A Bayesian Phylogenetic Model for Counting Recombination Events

We describe a Bayesian method for counting recom- bination events in the evolutionary history of aligned viral sequences when recombination is rare. Previ- ous recombination detection methods have focused on testing whether particular sequences are recombi- nant. Our method, in constrast, examines multiple recombinant sequences with the same recombinant structure and seeks to place a lower bound on the number of recombination events. Distinguishing the number of recombination events in the history of se- quences with similar structure will be necessary to nd recombination hotspots.