Core genome alignment of the Bacillaceae dataset. (A) Entire alignment; (B) a region around the comG operon that contains a local rearrangement; (C) a region around the replication origin; (D) a cluster of motility-related genes in which some of the genes are missing in the B. anthracis and B. cereus genomes. The rows and columns represent genomes and OGs, respectively. A black line represents a direct adjacency, a green line represents a non-adjacent neighborhood (i.e., there are insertions), and a red line represents an inversion. See Additional file 2 for the complete figures for both Bacillaceae and Enterobacteriaceae, which also contain the name of each OG.