Difference in prediction accuracies between GASP and three alternative algorithms. (a) Yang et al. 1995 ML , (b) Pupko et al. 2000  and (c) PAMP . Percentage Accuracies are calculated for variable sites only and only those phylogenies that did not crash CODEML are shown (see text for details). Positive values indicate GASP is better than the other algorithm and negative values the reverse. Results for each tree depth are calculated separately. Values shown are for 'PAM Variable Rates' simulations only but the other evolutionary models give very similar results (Data not shown).