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Table 7 Tree Accuracy Simulations. Results of the simulated tree accuracy test where alignments were generated with a particular model and then phylogenies were built using all of the other available models. Each entry is the average scaled Robinson-Foulds (RF) distance [40] over the trees inferred using the alternative models. This test was repeated 10 times for each model and the values in brackets are the RF distances from the true tree when phylogenies were inferred using the model that generated the alignment. Phyml [53] was used to build all trees.

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 RF Distance Model RF Distance
Blosum 0.03 (0.03) JTT 0.05 (0.05)
Blosum+I 0.02 (0.02) JTT+I 0.05 (0.04)
Blosum+G 0.08 (0.06) JTT+G 0.04 (0.03)
Blosum+I+G 0.05 (0.05) JTT+I+G 0.12 (0.11)
CPREV 0.05 (0.04) MtREV 0.06 (0.05)
CPREV+I 0.09 (0.04) MtREV+I 0.08 (0.08)
CPREV+G 0.06 (0.05) MtREV+G 0.07 (0.06)
CPREV+I+G 0.07 (0.06) MtREV+I+G 0.12 (0.1)
Dayhoff 0.07 (0.07) WAG 0.02 (0.02)
Dayhoff+I 0.06 (0.05) WAG+I 0.04 (0.04)
Dayhoff+G 0.06 (0.06) WAG+G 0.1 (0.1)
Dayhoff+I+G 0.05 (0.04) WAG+I+G 0.04 (0.04)