Relative frequencies of synonymous substitutions (Ks) for orthologs in three B. henselae strains. Each dot represents a triplet of orthologs, as determined by best reciprocal BLAST hits. The sum of the pair-wise Ks values for a triplet was normalized to one, and the proportion represented by each pair-wise comparison is plotted on the triangle plot, one for each axis. Tick marks indicate the direction of axis reading. Colors are log-proportional to the highest Ks value of the triplet, with yellow representing low Ks values and red high ones. The average of the dots is represented with a large black dot, and the values of the average Ks proportions are reported on the axes with black dots. Histograms showing the distribution of the Ks proportions are shown next to each axe. X-axis of the two upper histograms has been reversed to match the direction of the corresponding axes. See Additional file 7 for more details.