Table 1 Symbols used in estimating Ka and Ks
From: Computing Ka and Ks with a consideration of unequal transitional substitutions
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 |
g N | Frequency of nucleotide N, N ∈ {T, C, A, G} |
πj | Frequency of codon j, j ∈ {XYZ | X, Y, Z ∈ {T, C, A, G}} |