Figure 3.

Fragments of alignments of simulated sequences. Simulations were done with (a) or without (b) among-site rate heterogeneity. Both simulation were performed with Rose, following the tree represented in Figure 1 multiplied by a factor of 1.5. Positions of the alignments where more than 50% of the sequences are identical are shown with black boxes. The trees recalculated from the respective complete alignments are also shown, with the scale in amino acid substitutions/site. Interestingly, despite there being a very similar genetic distance between A and G in both alignments, A finds G by Blast in the alignment evolved under rate heterogeneity (A) but not in the alignment without rate heterogeneity (B).