Figure 1

Empirical data: relationship between ML consensus bootstrap proportion and Bayesian posterior probability. Comparison of PROML bootstrap proportions (horizontal axes) with Bayesian posterior probabilities (vertical axes) for all internal nodes in trees inferred from 21 empirical protein-sequence datasets. Data are for trees inferred by gamma-corrected ML under JTT, versus those inferred by gamma-corrected Bayesian inference under JTT (open diamonds) or under EQ (closed squares), (A) for the 7 datasets for which the two ML and two Bayesian trees (see text) are topologically identical, (B) for the 10 datasets for which at least one ML or Bayesian tree (see text) differs slightly (edit distance ≤ 2) from the other three, (C) for the 4 datasets for which at least one tree differs more substantially (edit distance ≥ 3), (D) for the subset of internal nodes, within the latter 14 non-identical trees, that subtend identical subtrees, and (E) for data in panels (A) and (D) plotted together.