CleanRecomb, a quick tool for recombination detection in SNP based cluster analysis

We present CleanRecomb, a tool to quickly filter a SNP matrix for likely recombination events.Method: The method evaluates segments with identical SNP profiles over the genome, based on the assumption that SNPs in the absense of recombination events are uniformly distributed across the genome. The method is evaluated on a set of 9 ST200 E. coli genome sequences.Results: The detected recombination events coincide with regions of elevated SNP density.