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Table 1 Coverage summary for simulation study

From: bModelTest: Bayesian phylogenetic site model averaging and model comparison

  Site Rate coverage Mean Subst. Model
Freqs model AC AG AT CG CT GT rate coverage
Equal plain 93 97 94 96 95 95 95 98
Equal +G 91 95 93 93 95 93 93.3 97
Equal +I 92 94 94 95 93 94 93.6 96
Equal +G+I 89 96 95 94 95 95 94 98
Unequal plain 96 95 96 97 93 96 95.5 96
Unequal +G 95 94 94 94 96 96 94.8 98
Unequal +I 89 94 95 95 93 95 93.5 93
Unequal +G+I 97 94 94 93 93 96 94.5 97
Mean   94.25 94.25 94.75 94.75 93.75 95.75 94.6 96
  Site Site model    Frequency Frequency coverage
Freqs model coverage α p inv coverage A C G T
Equal plain 100    100 100 100 100 100
Equal +G 96 94   100 100 100 100 100
Equal +I 98   95 100 100 100 100 100
Equal +G+I 99 89 88 100 100 100 100 100
Unequal plain 100    100 92 95 97 96
Unequal +G 97 94   100 97 92 92 98
Unequal +I 98   92 100 95 94 94 89
Unequal +G+I 100 93 91 100 99 96 96 98
Mean   98.75 93.50 91.50 100.00 97.38 97.88 97.13 97.38
  1. The first column lists the frequency and site models used to generate the data, and the last row is the mean coverage over all 800 runs. Coverage for rate parameters and frequencies is defined as the number of replicate simulations in which the true parameter value was contained in the estimated 95% HPD interval. The mean rate column contains the coverage averaged over all six rate coverage columns (i.e. the proportion of the 600 parameter estimates whose values were contained in their respective 95% HPD intervals. For details of substitution model coverage see text. The site model coverage is the number of replicate simulations that contained the correct model specification for rate heterogeneity across sites in the 95% credible set of models. Columns α and p inv are coverages of the shape and proportion invariable parameter conditioned on sampling from the true site model