Table 5 Id and Indel values for sequential and diverging evolution models

Test sets parameters Sequential evolution
id id id indel indel indel
N PAM (S0, S1) (S0, S2) Average (S0, S1) (S0, S2) Average
1000 30 0.7481 0.7499 0.7490 0.0324 0.0343 0.0334
1000 60 0.5788 0.5796 0.5792 0.0526 0.0560 0.0543
1000 120 0.3758 0.3770 0.3764 0.0740 0.0754 0.0747
10,000 30 0.7504 0.7501 0.7503 0.0330 0.0336 0.0333
10,000 60 0.5804 0.5807 0.5806 0.0526 0.0511 0.0519
10,000 120 0.3767 0.3762 0.3765 0.0755 0.0762 0.0759
Test sets
parameters
Divergent evolution
id PAM (id) indel PAM (indel)
N PAM (S1, S2) (S1, S2) (S1, S2) (S1, S2)
1000 30 0.5793 60.55 0.0662 68.56
1000 60 0.3756 122.25 0.1072 202.14
1000 120 0.2009 245.08 0.1473 >  830
10,000 30 0.5804 60.31 0.0661 68.30
10,000 60 0.3773 121.53 0.1023 170.52
10,000 120 0.2025 243.45 0.1490 >  830
1. N is the number of sequences in the test set, id is the identity fraction, indel is the proportion of insertion-deletions. Rows correspond to different values ​​of the PAM parameter. In the “Sequential evolution” block, the id (S0, S1) and id (S0, S2) columns show the proportion of matching positions in the alignments of the ancestor sequence with the descendant sequences; the indel (S0, S1) and indel (S0, S2) columns show the fraction of inserts for the same sequences. The “Divergent evolution” block in the columns id (S1, S2) and indel (S1, S2) shows the alignment characteristics of descendant sequences. The data are for sets of 1000 pairs of sequences and 10,000 pairs, the results differ by tenths of a percent