Fig. 6

Using fragments of pairwise alignments as an example, we present a scheme for generating a reference alignment in accordance with the model of divergent evolution. Here, the pairs (S0, S1) and (S0, S2) denote the generated alignments of the ancestral sequence S0 with the mutant sequences S1 and S2 generated from it, corresponding to an evolutionary distance of 120 PAM; (S1, S2) is the resulting pair alignment corresponding to the scheme of divergent evolution

Further, for simplicity, the distance between S1 and S2 is denoted by the corresponding distance of sequential evolution (in this example, 120PAM), although the true distance between S1 and S2 is almost two times greater (see Table 5).