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Table 3 Average ω estimates calculated based on YN, MYN and γ-MYN.

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

Rice Codon Frequencies (α = 4)
Number of codons ω = 0.2 ω = 0.3
  YN MYN γ-MYN YN MYN γ-MYN
100 0.308 0.245 0.235 0.458 0.364 0.352
200 0.305 0.230 0.222 0.450 0.341 0.332
300 0.294 0.219 0.210 0.435 0.325 0.316
400 0.290 0.215 0.207 0.426 0.317 0.308
500 0.294 0.216 0.208 0.430 0.317 0.308
600 0.291 0.214 0.206 0.427 0.316 0.307
700 0.290 0.213 0.205 0.424 0.313 0.305
800 0.290 0.212 0.205 0.424 0.313 0.305
900 0.288 0.212 0.204 0.422 0.312 0.303
1000 0.287 0.210 0.203 0.421 0.310 0.302
  1. Note: The parameters used are κR = 10, κY = 1, t = 0.6, and α = 4. ω = 0.2 and ω = 0.3 are used separately to represent purifying selection. ω values are averaged over 2,000 pairs of simulated sequences.