Sequence conservation -or phylogenetic footprintingprovides a powerful approach for identifying potential functional noncoding sequences, and has been used in a variety of eukaryotic and prokaryotic organisms to identify protein coding genes, noncoding RNAs, and regulatory elements [57, 58] . For optimal power, the organisms being analyzed must be sufficiently distant such that non-functional elements have diverged, but not so distant such that functional elements have evolved or re-arranged. Organisms within the Mtb complex are all highly similar at the sequence level, and thus by themselves do not allow for effective phylogenetic footprinting. By leveraging the evolutionary similarity of the most distantly related Mycobacteria and Actinomycetes, we gained additional power to allow us to detect functional sequences under purifying selection, albeit only those shared by at least a majority of Mycobacteria. We used this approach to predict two classes of conserved noncoding sequences: small noncoding RNAs and transcription factor binding motifs.