Equal-Constraint-n-F-dGm(r|s|sf) | Equal constraint irrespective of amino acid substitution type is assumed; β = 0 in Eq. 4. |
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EI-n-F-dGm(r|s|sf) | ) based on the Energy-Increment-based (EI) method [26] is used to estimate w ab in Eq. 4. The and represent the effects of the mean increment of contact energy between residues and of residue-volume change due to an amino acid replacement, respectively; see Supporting Information, Text S1, in [26]. |
JTT-ML91+-n-F-dGm(r|s|sf), WAG-ML91+-n-F-dGm(r|s|sf), LG-ML91+-n-F-dGm(r |s|sf) | Selective constraints estimated by maximizing the likelihood of JTT/WAG/LG [5, 10, 11] in the ML-91+ model [26] are used as in Eq. 4. |
KHG-ML200-n-F-dGm(r|s|sf) | Selective constraints estimated by maximizing the likelihood of the KHG codon substitution matrix [25] in the ML-200 model [26] are used as in Eq. 4. |