Molecular tree of four completed genomes. Molecular tree of E. coli (Ec), H. influenzae (Hi), M. genitalium (Mg), and B. subtilis (Bs) were reconstructed by the protein distance matrix (A) and the 16S rRNA (B) analysis. Molecular trees reconstructed by two different methods are compared and show agreement each other. The methodology using protein distances of whole genome sequences could successfully estimate the evolutionary relationship among the four complete genomes. The bootstrap score (1000) is shown for the 16S rRNA analysis.