Table 1 Parameter estimates, likelihood scores and identified selected sites under various models. Branch numbers refer to Figure 4A. Parameters indicating positive selection are in bold. A likelihood ratio test (LRT) is used to compare a pair of nested models: one which accounts for sites with ω > 1 and one which does not (the null model). To accept or reject the ω > 1 hypothesis, twice the log-likelihood difference in the scores is compared with a χ2 distribution with the degrees of freedom equal to the difference in the numbers of parameters between the two models. When ML detects lineages with ω > 1, an empirical Bayes analysis identifies sites under positive selection and calculate posterior probabilities that provide a measure of confidence for that prediction.
From: Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study
Model | p | l | Parameter estimates | Positively selected sites | Likelihood Ratio Test |
|---|---|---|---|---|---|
M0:one ratio | 1 | -11903.5 | ω = 0.0418 | none |  |
Site-specific models | Â | Â | Â | Â | Â |
   M1:neutral (K = 2) | 1 | -13195.5 | p0 = 0.298, p1 = 0.702 | not allowed |  |
   M3:discrete (K = 2) | 3 | -11627.6 | p0 = 0.6, p1 = 0.4, ω0 = 0.012, ω1 = 0.098 | none |  |
Branch-site models | Â | Â | Â | Â | Â |
   Branch 1 |  |  |  |  |  |
Model A | 3 | -13160.0 | p0 = 0.3, p1 = 0.70, p2+p3 = 0, ω2 = 0 | none |  |
Model B | 5 | -11627.6 | p0 = 0.4, p1 = 0.6, p2+p3 = 0 ω0 = 0.098, ω1 = 0.012, ω2 = 0 | none |  |
   Branch 2 |  |  |  |  |  |
Model A | 3 | -13188.7 | p0 = 0.296, p1 = 0.688, p 2 +p 3 = 0.016, ω 2 = 129.6 | Q157 (P = 0.77), Q203 (P = 0.999), T41, Q157, Y184, N200, Q203, R284 (P > 0.9) | LRT vs. M1 2Δl = 6.8, P = 0.03, df = 2 |
Model B | 5 | -11621.4 | p0 = 0.356, p1 = 0.59, p 2 +p 3 = 0.05 ω0 = 0.1, ω1 = 0.0125, ω 2 = 9.7 |  | LRT vs. M3 (K = 2) 2Δl = 6.2, P = 0.04, df = 2 |