Table 8 Proteobacteria Tree Accuracy Analysis. The scaled Robinson-Foulds (RF) distances [40] of the trees produced from the Proteobacteria dataset using fixing a model used to build trees from each alignment. The values reported are the median and average distance computed by comparing every tree against every other tree. When the optimal set of models were used the median was 0.22 and the average was 0.34. 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