Alcaraz et al. BMC Genomics 2010, 11:332 http://www.biomedcentral.com/1471-2164/11/332 Page 6 of 17 Figure 2 Phylogenetic reconstruction for Bacillus. A. Concatenated 814 translated genes of the core genome maximum likelihood (ML) phylogeny. Bootstrap values are shown. B. Genome Similarity Score (GSS) distance matrix plotted as a Neighbor-Joining tree. C. ML phylogeny using 16S rRNA. C. Concatenated 20 Conserved Universal Cogs (uCOGs) ML phylogeny. Note how inner groups are well defined and supported only in the core genome phylogeny (A) and how the GSS distance (B) resembles the inner groups described in the core’s genome phylogeny.