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Table 5 Amino Acid Frequency Simulations. Results of the simulated datasets where the original amino acid frequencies are randomly perturbed by up to 10% from the original values and the alignment length is 500 characters. Each entry indicates the number of times out of 100 replicates the correct model was selected by each measure.

From: Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Model AIC1 AIC2 BIC Model AIC1 AIC2 BIC
Blosum+F 94 100 100 JTT+F 93 100 100
Blosum+I+F 71 91 95 JTT+I+F 67 89 94
Blosum+G+F 86 93 96 JTT+G+F 75 89 92
Blosum+I+G+F 99 97 96 JTT+I+G+F 98 96 96
CPREV+F 92 100 100 MtREV+F 93 99 99
CPREV+I+F 87 98 99 MtREV+I+F 86 96 99
CPREV+G+F 93 96 97 MtREV+G+F 86 93 95
CPREV+I+G+F 89 87 84 MtREV+I+G+F 85 82 80
Dayhoff+F 93 99 99 WAG+F 95 100 100
Dayhoff+I+F 91 98 99 WAG+I+F 82 96 97
Dayhoff+G+F 86 93 96 WAG+G+F 88 95 96
Dayhoff+I+G+F 99 97 96 WAG+I+G+F 90 89 89