Table 1.

Symbols used in estimating Ka and Ks

Symbol	Definition
S	Number of synonymous sites
N	Number of nonsynonymous sites
Sd	Number of synonymous substitutions
Nd	Number of nonsynonymous substitutions
Ks	Synonymous substitution rate
Ka	Nonsynonymous substitution rate
ω	Estimator of selective strength, ω = Ka/Ks
t	Divergence time between two sequences, the expected number of nucleotide substitutions per codon, t = (Ks × 3S + Ka × 3N)/(S + N)
αR	Transitional rate between purines
αY	Transitional rate between pyrimidines
α	Transitional rate
β	Transversional rate
κR	Ratio of transitional rate between purines to transversional rate, κR = αR/β
κY	Ratio of transitional rate between pyrimidines to transversional rate, κY = αY/β
κ	Ratio of transitional rate/transversional rate, κ = α/β
gN	Frequency of nucleotide N, N ∈ {T, C, A, G}
πj	Frequency of codon j, j ∈ {XYZ | X, Y, Z ∈ {T, C, A, G}}