We evaluated PhyloScan on both real and synthetic data. For the real data, we chose the Escherichia coli Crp and PurR motifs, and we gathered genome sequence data for several gamma-proteobacteria. We and others have previously demonstrated that a comparative genomic approach is effective in the prediction of transcription factor binding sites within this phylogenetic group [17-26]. Among the species chosen for this study (E. coli, Salmonella enterica serovar Typhi (S. typhi), Yersinia pestis, Haemophilus influenzae, Vibrio cholerae, Shewanella oneidensis, and Pseudomonas aeruginosa), only E. coli and S. typhi exhibit sufficient homology in the promoter regions [26]. Thus, we aligned orthologous intergenic regions for these two species, and we combined the statistical evidence from the scanning of the aligned E. coli and S. typhi data with the statistical evidence from the scanning of unaligned orthologous intergenic regions from the remaining five, more distantly related, species. (Approaches in which the S. typhi sequence data is considered independent of the E. coli sequence data were considered in earlier work [26].)