2. All non-Mycobacteria in our set (excluding Nocardia and Rhodococcus because of their similarity to Mycobacteria 6. R. jostii RHA1 and N. farcinia We calculated differences between two sets of organisms exactly as we calculated distances between clusters (above). However, rather than using different clusters of organisms determined by k-means clustering, we used these pre-defined clusters of organisms. We looked at distances between the following sets of organisms: 1-2, 3-4, 3-5, 3-6, 4-5, 4-6, 5-6. For each PFAM domain or GO term represented in at least two organisms in these pairings, we calculated p-values for the differences between the profile values by T-test (Bonferroni-corrected by the number of PFAM domains represented in that set of organisms) and computed inter-and intra-centroid distances (as described in the above paragraph). We compiled lists of those that are most expanded and a list of those most contracted across these pairings. On our website we have included complete lists of PFAM categories, including those that do not make the strict Bonferroni-corrected p-value cutoff. Many potentially interesting expansions do not make the overly conservative Bonferroni-corrected p-value cutoff [95, 96] .