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 |
S_{d} | Number of synonymous substitutions |
N_{d} | 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 |
κ_{R} | Ratio of transitional rate between purines to transversional rate, κ_{R} = α_{R}/β |
κ_{Y} | Ratio of transitional rate between pyrimidines to transversional rate, κ_{Y} = α_{Y}/β |
g_{N} | Frequency of nucleotide N, N ∈ [T, C, A, G] |
α_{R} | Transitional rate between purines |
α_{Y} | Transitional rate between pyrimidines |
β | Transversional rate |