Figure 3.

Phylogenetic signal of gaps. (a) Assessment of gap accuracy under default parameters using the species-tree discordance test with parsimony trees on presence/absence patterns of gap characters in aminoacid alignments. By taking into account gap information, this test demonstrates that the gap placement of Prank is significantly better than other alignment methods. This cannot be observed either using standard tree building methods (Figure 2), or using structure-based benchmarks. Error bars correspond to ± 1 s.d. Significant difference from Prank is denoted with a minus symbol at the basis of relevant bars (Wilcoxon double-sided test, P < 0.01). (b) Accuracy of maximum likelihood (ML) trees on amino-acid substitution patterns versus parsimony on binary gap presence/absence characters, on fungal data. The phylogenetic signal of gaps inferred by Prank increases with divergence. For distant sequences, the proportion of correctly inferred splits from gaps alone is close to that from amino-acids substitutions by ML. Thus, tree building methods could capture up to twice as much phylogenetic signal from the same data. Moreover, note that the crude approach used here to infer the gap trees likely understates the potential of gap patterns.