Figure 1

Stack distributions of FDP. Values are drawn in blue and purple for real and simulated data, respectively. Histograms are plotted for the 105 pairwise comparisons from the mt336 dataset (A) and the 10 pairwise comparisons from the nuc80 dataset (B). Simulation values were averaged over ten simulated datasets and only variable positions (i.e. two or more substitutions per site), which have sufficient phylogenetic signal for profile affiliation, were considered.