Stratification of co-evolving genomic groups using ranked phylogenetic profiles

BMC Bioinformatics

Table 1 Taxonomic classification and number of proteins of the fully sequenced species analyzed.

Species	Taxonomy†	Taxonomic relatedness to *M. genitalium*	Evaluation of the divergence distance from *M. genitalium*‡	Number of proteins
Mycoplasma genitalium	Bacteria; Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae; Mycoplasma	-	0	480
Ureaplasma parvum	Bacteria; Firmicutes; Mollicutes; Mycoplasmatales; Mycoplasmataceae; Ureaplasma	Within family	17	611
Streptococcus pyogenes	Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae; Streptococcus	Within phylum	25	1696
Buchnera aphidicola	Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Buchnera	Within superkingdom	31	574
Nanoarchaeum equitans	Archaea; Nanoarchaeota; Nanoarchaeum	From distinct super kingdoms	59	536

† The taxonomic classification is according to http://www.ncbi.nlm.nih.gov/Taxonomy/. The common path between each and M. genitalium is shown in bold.
‡ The evaluated divergence distance aims to provide a quantitative assessment of the taxonomic distance. The values are derived from the scores of the pair-wise alignments between the 16S RNA from each species and the 16S RNA from M. genitalium (see Methods). The same divergence order was obtained when distance matrix was retrieved from greengenes - a 16s RNA gene database [38] (divergence distance scores ordered as in the table: 0, 0.14, 0.25, 0.31, 0.63, see Methods).

ISSN: 1471-2105