Why does PAUP* warn me that the stepmatrix supplied in Xu and Miranker (2004, “A metric model of amino acid substitution”, Bioninformatics 20:1214-1221) is “internally inconsistent”?
Symmetric stepmatrices in PAUP* are required to satisfy the triangle inequality. If they fail to do so, a warning is issued and the costs in the matrix are adjusted until the triangle inequality is satisfied for all possible triplets of states. Unfortunately, the matrix given in the paper by Xu and Miranker contained a minor error. A corrected matrix is available at the following location: http://www.cs.utexas.edu/users/mobios/Publications/mPAMErrata.pdf.
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