Maximum likelihood estimates of <i>d_N</i> and <i>d_S</i> using codon-based models.

1)<p>Assuming that M₀ is true null hypothesis (<i>Η</i>₀) with <i>p</i>₀ parameters and that M₃ is the alternative hypothesis (<i>Η</i>₁) with <i>p</i>₁ parameters. The log likelihood difference <b><i>2Δℓ = 2(ℓ₁−ℓ₀)</i></b> follows asymptotically a χ² distribution with (<i>p</i>₁−<i>p</i>₀) degrees of freedom.</p>*)<p>Best-fitted model according to the likelihood ratio test (LRT) between of M₀ vs. M₃ with 4 degrees of freedom.</p>$)<p>Best-fitted model according to the likelihood ratio test (LRT) between of M₂ vs. M₃ with 1 degree of freedom.</p>#)<p>Positively selected sites were detected according to the Naive Empirical Bayes method with p≥0.99. Sites 33 and 44 (underlined) correspond respectively to sites 11 and 25 of V3 loop; which are related with R5-to-X4 change.</p>∶)<p>This result was obtained using unique sequences and X4-strains because exclusion of them did not affect on the model preference or the parameter values.