Figure 5
From: Multiple sequence alignment accuracy and evolutionary distance estimation
Evolutionary distance estimates versus position of third sequence. Estimated evolutionary distance of sequences A and B from the true, pair wise and three-taxon multiple alignments. Expected distance of sequences A and B was (A) d = 0.5; (B) d = 1.0; (C) d = 2.0. Lengths of branches x and y are illustrated in Figure 8. All points are averages of 1,000 simulation replicates. The X in panel (B) marked by an arrow indicates the mean distance estimate obtained for the three-taxon multiple alignments when Clustal was forced to use the correct guide tree rather than an estimating its own from the data; see the text for more information.