Phylogenetic trees of five S. salmonicida genes from the phylogenomic analysis. ML tree of conceptually translated, aligned amino acid positions of (A) arginine deiminase, (B) conserved hypothetical protein, (C) conserved hypothetical protein, (D) carotenoid isomerase, and (E) rubrerythrin. Bootstrap support values > 50% are shown. Details about the phylogenetic analyses are found in the Methods section, and complete accession numbers and complete species names are found in Additional files 4 and 6. The unrooted trees are arbitrarily rooted for the presentation. The branches and species names are labeled according to their phylogenetic classification: Archaea (red), proteobacteria (grey), low G+C Gram positives (blue), cyanobacteria (green), and other eubacterial lineages (black). Eukaryotes are in boldface and labeled according to their classification into super-groups : Opisthokonta (orange), Amoebozoa (purple), Chromalveolata (red), Archaeplastida (green), and Excavata (brown).