Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates

Table 5 Sensitivity of false positive rates to the choice of model parameterization under the nine different null scenarios of Simulation Studies 1–3

Scenarios 1a and 1b are based on a 5-taxon tree, and 2a, 2b and 3a are based on a 17-taxon tree (see Fig. 1). GY denotes the frequency parameterization of Goldman and Yang [26] where the transition probability is proportional to target codon. MG denotes the frequency parameterization Muse and Gaut [47] where the transition probability is proportional to target nucleotide. Both require frequency estimates for the four nucleotides at each position of the codon (denoted F3 × 4), and thus each requires 9 free parameters

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