Evaluation of the accuracy and power of the likelihood tests for positive selection using simulated data
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Data simulated under the same global parameters as the real data, with sites evolving under a mix of purifying selection and neutrality (Nearly Neutral model); plus sites under positive selection on the foreground branch for the positive selection model. Simulations under the Nearly Neutral model with original branch lengths divided by 2 are not shown, because 0% of tests are significant for all branches.
aClassification of topologies and branches following Figure 1. FSGD, fish-specific genome duplication.
bNumber of trees where the model A with foreground ω2 > 1 is significantly more likely than the model A with ω2 = 1, with multiple test correction by the q-value of Storey and Tibshirani (2003). (LRT) Likelihood ratio test.
cThe number of trees with at least one branch where positive selection was significant.
