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.

We have also shown that when amino acid frequencies deviate from the default amino acid frequencies of each model, there is a clear trend towards the '+F' version of each model.

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Table 5 shows that when the original model amino acid frequencies were randomly perturbed, there was a definite trend among all of the model selection measures to select the corresponding '+F' version of the particular model over the original models.

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