Figure 4.

Estimated correlation $\left(r=\widehat{\rho }\right)$ between pairwise estimates of ω and d, for the case of two sequences evolving according to the standard genetic code. The pairwise alignments were simulated with the program EVOLVER, with equal codon frequencies (1/61) and κ = 2. Maximum-likelihood estimates were obtained with CODEML. The dashed lines indicate the true values of ω and d used in the simulations. For some simulated alignments the MLE of d or ω may be ∞. CODEML outputs these values as 50 and 99, respectively. These values are not used in the calculation of r.