Figure 2

Improvement in alignment accuracy in multiple versus pair wise alignment. Absolute improvement in accuracy of alignment of sequences A and B in the multiple (ABC) alignment versus the pair wise (AB) alignment. Improvement was measured as ABC – AB, where ABC indicates the accuracy of the alignment of sequences A and B in the multiple alignment and AB indicates the accuracy of the alignment of these sequences in the pair wise alignment. 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. Error bars represent 95% confidence limits.