Table 2 Full ML Comparison. A comparison of the models selected from the likelihood values obtained from a full ML tree search using all models and the likelihood values using the default NJ-JTT base tree. The column 'Identical' indicates the number of times (out of 100 alignments) both procedures selected the same model. The column titled 'Rate' indicates cases when the same amino acid matrix and a different ASRV was selected. The column titled 'Matrix' indicates cases when the a different amino acid matrix 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