Maximum likelihood inference of protein phylogeny and the origin of chloroplasts

@article{Kishino2005MaximumLI,
  title={Maximum likelihood inference of protein phylogeny and the origin of chloroplasts},
  author={Hirohisa Kishino and Takashi Miyata and Masami Hasegawa},
  journal={Journal of Molecular Evolution},
  year={2005},
  volume={31},
  pages={151-160}
}
SummaryA maximum likelihood method for inferring protein phylogeny was developed. It is based on a Markov model that takes into account the unequal transition probabilities among pairs of amino acids and does not assume constancy of rate among different lineages. Therefore, this method is expected to be powerful in inferring phylogeny among distantly related proteins, either orthologous or parallogous, where the evolutionary rate may deviate from constancy. Not only amino acid substitutions but… 
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