Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.

@article{Yang1997BayesianPI,
  title={Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.},
  author={Z Yang and Bruce Rannala},
  journal={Molecular biology and evolution},
  year={1997},
  volume={14 7},
  pages={
          717-24
        }
}
An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data. The birth-death process with species sampling is used to specify the prior distribution of phylogenies and ancestral speciation times, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree. Monte Carlo integration is used to integrate over the ancestral speciation times for particular trees. A Markov Chain Monte Carlo method is used to… 

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