Empirical evaluation of a prior for Bayesian phylogenetic inference.

@article{Yang2008EmpiricalEO,
  title={Empirical evaluation of a prior for Bayesian phylogenetic inference.},
  author={Ziheng Yang},
  journal={Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
  year={2008},
  volume={363 1512},
  pages={4031-9}
}
The Bayesian method of phylogenetic inference often produces high posterior probabilities (PPs) for trees or clades, even when the trees are clearly incorrect. The problem appears to be mainly due to large sizes of molecular datasets and to the large-sample properties of Bayesian model selection and its sensitivity to the prior when several of the models under comparison are nearly equally correct (or nearly equally wrong) and are of the same dimension. A previous suggestion to alleviate the… CONTINUE READING

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