Figure 3

Relative improvement in alignment accuracy in multiple versus pair wise alignment. Relative improvement in accuracy of alignment of sequences A and B in the multiple (ABC) alignment versus the pair wise (AB) alignment. Relative improvement was measured as (ABC – AB) / 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. d indicates the expected distance between sequences A and B. Lengths of branches x and y are illustrated in Figure 8. All points are averages of 1,000 simulation replicates.