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Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method
2002
Molecular biology and evolution
Evolution of proteins is generally modeled as a Markov process acting on each site of the sequence. Replacement frequencies need to be estimated based on sequence alignments. Here we compare three approaches: First, the original method by Dayhoff, Schwartz, and Orcutt (1978) Atlas Protein Seq. Struc. 5:345-352, secondly, the resolvent method (RV) by Müller and Vingron (2000) J. Comput. Biol. 7(6):761-776, and finally a maximum likelihood approach (ML) developed in this paper. We evaluate the
doi:10.1093/oxfordjournals.molbev.a003985
pmid:11752185
fatcat:eaxdyscpercoxky5tdqm2xybyi