Phylogenetic tree construction using markov chain monte carlo

Shuying Li, Dennis K. Pearl, Hani Doss

Research output: Contribution to journalArticlepeer-review

142 Scopus citations


We describe a Bayesian method based on Markov chain simulation to study the phylogenetic relationship in a group of DNA sequences. Under simple models of mutational events, our method produces a Markov chain whose stationary distribution is the conditional distribution of the phylogeny given the observed sequences. Our algorithm strikes a reasonable balance between the desire to move globally through the space of phylogenies and the need to make computationally feasible moves in areas of high probability. Because phylogenetic information is described by a tree, we have created new diagnostics to handle this type of data structure. An important byproduct of the Markov chain Monte Carlo phylogeny building technique is that it provides estimates and corresponding measures of variability for any aspect of the phylogeny under study.

Original languageEnglish (US)
Pages (from-to)493-508
Number of pages16
JournalJournal of the American Statistical Association
Issue number450
StatePublished - Jun 1 2000

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Statistics, Probability and Uncertainty


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