Among the species included in this study, only E. coli and S. typhi exhibit extensive homology (70% identity on average) in the promoter regions [26]. The phylogenetic distance of two sequences that share this level of homology is 0.384, assuming the nucleotide substitution model of Jukes & Cantor [45] (and the value would be similar under a variety of more current models); thus, we assumed this phylogenetic distance between E. coli and S. typhi, and data from these two species are taken to form one clade for PhyloScan. Each of the remaining species formed a separate clade of unaligned sequence data, since these species do not exhibit sequence identity with E. coli or with each other [26].