Because of the similarity of the genomes within the Mtb complex, we were not able to resolve the phylogeny using only these 177 proteins that are uniform across all 31 organisms. In order to better resolve the tree within the Mtb cluster, we computed a separate tree using 1747 orthogroups that are uniform across the Mtb cluster and M. ulcerans, which we used as an outgroup. Using this expanded gene set, we were able to resolve the tree for the Mtb cluster.