These two-ratio models were also compared against the null model (one ratio model) by LRT.
The null model (one ratio) assumed equal ω for all branches.
To test for variable selective pressures among branches, we performed the branch model using either the null model (one ratio) or nested models (two-ratio, three-ratio, and four-ratio models) (Yang 1998; Bielawski and Yang 2003).
The simplest model (one ratio), a very strict model allowing a single ω for all branches, obtained a ω = 1.2934, providing a good support for positive selection in the primate ANG.
The branch specific models, One-ratio (R1) and Two-ratios (R2) were used to detect lineage-specific changes in selective pressure.
Using Codeml from PAML the branch specific models, One-ratio (R1) and Two-ratios (R2) were used to detect lineage-specific changes in selective pressure after the duplication events.
The ratio of nonsynonymous-to-synonymous for each branch under two models (one-ratio and free-ratio for branches) was calculated, and the two models were compared using the LRT test to see whether the ω ratios are different among lineages.
Varying selective pressure along the genes was assessed by a LRT test comparing the site-specific model M3 (discrete) with 2 or 3 classes of sites displaying different ω, against the M0 model (one-ratio).
In this study, the basic model (one-ratio), two site-specific models (nearly-neutral and positive-selection) and the branch-site model A were applied on each tree.
Twice the log likelihood difference between models, 2Δℓ = 2 ℓ1-ℓ0), is compared to a χ-distribution with the degrees of freedom equal to the number of parameter differences between the models to test whether the alternative model (free-ratio or PD-PS) fits the data significantly better than the null model (one-ratio).
The reduced alignment of the bovine BSP30 and human and mouse PSP genes were fitted with two maximum likelihood models, namely one ratio and two-ratio models.
