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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.
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Biology Direct

ISSN: 1745-6150

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