Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method.

@article{Mller2002EstimatingAA,
  title={Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method.},
  author={Tobias M{\"u}ller and Rainer Spang and Martin Vingron},
  journal={Molecular biology and evolution},
  year={2002},
  volume={19 1},
  pages={8-13}
}
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… CONTINUE READING
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