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Table 1 Symbols used in Ka and Ks calculation

From: γ-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates

Symbol Definition
S Number of synonymous sites
N Number of nonsynonymous sites
Ks Synonymous substitution rate
Ka Nonsynonymous substitution rate
ω Estimator of selective strength, ω = Ka/Ks
Sd Number of synonymous substitutions
Nd Number of nonsynonymous substitutions
t Divergence time between two sequences, the expected number of nucleotide substitutions per codon, t = (Ks × 3S + Ka × 3N)/(S + N)
α The parameter of gamma distribution
κ Ratio of transitional rate/transversional rate
κR Ratio of transitional rate between purines to transversional rate, κR = αR
κY Ratio of transitional rate between pyrimidines to transversional rate, κY = αY
gN Frequency of nucleotide N, N [T, C, A, G]
αR Transitional rate between purines
αY Transitional rate between pyrimidines
β Transversional rate