Instances of expanded or missing pathways across the 31 organisms will have non-uniform pathway-level phylogenetic profiles. Thus we tabulated the number of genes in each genome for each category, and automatically searched for gene categories whose copy number (normalized for genome size) had the most non-uniform distribution across the 31 organisms in order to identify the most significant examples of expansions or losses. To identify categories with bimodal properties (such as a categories with a loss or a large expansion on only certain branches of the phylogenetic tree), we clustered each profile into two groups and looked for the pathways with the greatest separation between the two clusters. We used k-means (k = 2) to cluster the profile vectors, and compared the intra-and inter-cluster point-to-centroid distances to find the clusters with the greatest separation. We ranked categories by this separation to find bimodal categories. We further select those that have at least five organisms in the smallest of the two clusters, and an average of at least five genes per genome. P-values are calculated from a T-test between the values for the two groups, with Bonferroni correction applied. In our Supplementary Information website we list those categories with p < 0.05, ranked by the difference between their inter-to intra-centroid distances. When we select the metabolic pathways, PFAM domains, and GO terms with the most non-uniform category-level phylogenetic profiles overall, we find that many of the top categories are lipid metabolism-related categories expanded in the Mycobacteria.