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Table 4 Gamma Distribution Simulations. Results of simulations when the α parameter of the gamma distribution was varied between 0.5, 1.0, and 2.0. The sequence length was kept constant at 500 characters and the proportion of invariable sites was 0.2. Each entry is the number of times out of 100 replicates that the correct model was selected.

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

  α = 0.5 α = 1.0 α = 2.0
Model AIC1 AIC2 BIC AIC1 AIC2 BIC AIC1 AIC2 BIC
BLOSUM62+G 75 83 87 32 62 69 36 68 74
BLOSUM62+I+G 90 88 87 95 93 92 100 100 100
CPREV+G 89 89 90 39 72 77 39 65 79
CPREV+I+G 80 75 73 93 89 89 100 100 100
Dayhoff+G 77 86 90 33 36 74 38 60 66
Dayhoff+I+G 82 74 74 98 95 92 100 100 100
JTT+G 78 85 86 43 71 76 25 54 63
JTT+I+G 89 85 82 98 96 94 100 100 100
MtREV+G 92 94 95 46 72 76 51 75 84
MtREV+I+G 68 65 61 90 85 83 100 100 100
WAG+G 83 89 89 35 70 76 32 70 79
WAG+I+G 79 73 69 97 91 90 100 100 100
Dayhoff+I+G 54 35 38 82 74 74 95 92 91
JTT 95 98 98 94 99 100 93 98 100
JTT+I 95 99 98 96 100 100 96 100 100
JTT+G 87 94 94 78 85 86 91 91 93
JTT+I+G 48 36 40 89 85 82 96 95 94
MtREV 95 98 98 85 96 97 91 97 97
MtREV+I 97 100 100 92 99 100 97 100 100
MtREV+G 86 97 97 92 94 95 92 95 96
MtREV+I+G 29 17 17 68 65 61 87 85 83
WAG 91 97 96 88 97 99 97 98 100
WAG+I 94 100 99 98 100 100 97 99 100
WAG+G 85 95 93 83 89 89 86 95 95
WAG+I+G 50 34 36 79 73 69 97 96 94