ClonalFrame (version 1.2)23 was run at 40,000 iterations on the whole genome core nucleotide alignment identified by progressive MAUVE with all 43 genomes, and the initial half was discarded as Markov Chain Monte Carlo (MCMC) burn in. Good convergence and mixing properties were found between the four runs, making sure that they produced consistent estimates of the global parameters, clonal genealogy and location of recombination events. Additionally, for each reconstructed branch substitution event introduced by either mutation or recombination, the number of mutation events, and the number of recombination events were approximated. The relative effect of recombination and mutation on genetic change (r/m) and the relative rate of mutation and recombination (ρ/θ) were estimated. We also implemented two separate runs of ClonalFrame using the whole genome alignment of only the Lp serogroups (25 genomes) and non-Lp species (18 genomes) to obtain L. pneumophila specific recombination parameters.