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Bastien, O., Roy, S. and Marechal, E., 2005. Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions. C R Biol, 328(5): 445-453.

Catanzaro, D., Pesenti, R. and Milinkovitch, M.C., 2006. A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model. Bioinformatics, 22(6): 708-715.

Dayhoff, M.O., 1979. Survey of new data and computer methods of analysis. Atlas of Protein Sequence and Structure, 5(Suppl. 3): 1-8.

Dayhoff, M.O. and Eck, R.V., 1968. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure, 1: 33-45.

Dayhoff, M.O., Eck, R.V. and Park, C.M., 1972. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure, 5: 89-99.

Holmquist, R., Goodman, M., Conroy, T. and Czelusniak, J., 1983. The spatial distribution of fixed mutations within genes coding for proteins. J Mol Evol, 19: 437-448.

Melo, F. and Marti-Renom, M., 2006. Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets. Proteins.

Miyata, T. and Yasunaga, T., 1980. Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J Mol Evol, 16: 23-36.

Schwartz, R.M. and Dayhoff, M.O., 1978. Detection of distant relationships based on point mutation data. In: H. Matsubara and T. Yamanaka (Editors), Evolution of Protein Molecules. Japan Scientific Society, Tokyo, pp. 1-16.

Schwartz, R.M. and Dayhoff, M.O., 1978. The point mutation process in proteins. In: H. Noda (Editor), Origin of Life. Center for Academic Publications, Tokyo, pp. 457-469.

Schwartz, R.M. and Dayhoff, M.O., 1979. Matrices for detecting distant relationships. Atlas of Protein Sequence and Structure, 5(Suppl. 3): 353-358.

Uzzel, T. and Corbin, K.W., 1971. Fitting discrete probability distribution to evolutionary events. Science, 172: 1089-1096.


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