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/β |
κY | Ratio of transitional rate between pyrimidines to transversional rate, κY = αY/β |
gN | Frequency of nucleotide N, N ∈ [T, C, A, G] |
αR | Transitional rate between purines |
αY | Transitional rate between pyrimidines |
β | Transversional rate |