On average, the genome of B. atrophaeus is approximately 86% identical to B. subtilis on the nucleotide level,supporting its delineation as a distinct species and agreeing well with previous estimates [29] . Analysis of the IBGD using whole-genome sequences (N-mer length .4) supported the identification of B. subtilis 168 as the closest relative among sequenced bacterial genomes ( Figure 3 ). For this particular case, n = 5 (i.e., there were 4 5 = 1024 total 5-mers used to compute the IBGD). The IBGD values were relatively insensitive to the choice of n over the range of 4-8. Thethree BGgenomes analyzed grouped closely together, and our analysis of the Bacillus-wide phylogeny using IBGD revealed the phylogenetic distance of that B. subtilis/B. atrophaeus species from B. anthracis, supporting the inferences published elsewhere from rRNA sequence analysis ( Figure 3 ) [30] . Primary amino acid sequences of RAST-annotated proteins are on average 72% (median 83%) identical between B. atrophaeus and B. subtilis. When only the proteins that yielded bidirectional BLAST hits in RAST are examined, the predicted proteome of B. atrophaeus is, on average, 83% identical (86% median) to B. subtilis.