Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference

@article{Rannala2006ProbabilityDO,
  title={Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference},
  author={Bruce Rannala and Ziheng Yang},
  journal={Journal of Molecular Evolution},
  year={2006},
  volume={43},
  pages={304-311}
}
A new method is presented for inferring evolutionary trees using nucleotide sequence data. The birth-death process is used as a model of speciation and extinction to specify the prior distribution of phylogenies and branching times. Nucleotide substitution is modeled by a continuous-time Markov process. Parameters of the branching model and the substitution model are estimated by maximum likelihood. The posterior probabilities of different phylogenies are calculated and the phylogeny with the… 
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