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MrBayes: Bayesian Inference of Phylogeny

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Other programs for Bayesian estimation of phylogeny:

  • BAMBE A nice program by Bret Larget and Donald Simon for the Bayesian inference of phylogeny.
  • Mac5 A program by Paul-Michael Agapow that deals with gaps as a fifth state. This link is temporary disabled?
  • Beast BEAST, written by Alexei Drummond and Andrew Rambaut, is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is particularly good for molecular clock analyses.
  • PHASE Paul Higgs is the author of Phase, designed specifically for use with RNA sequences that have a conserved secondary structure, e.g. rRNA and tRNA.

Tools for use with MrBayes:

  • MrModeltest2 A program by Johan Nylander for selecting DNA substitution models.

Programs for the maximum likelihood estimation of phylogeny:

  • PAUP* David Swofford's program implements the maximum likelihood method under a number of nucleotide models.
  • PAML Ziheng Yang's program implements virtually every model of molecular evolution that has been proposed. (This is not surprising as he invented many of them.)
  • PHYLIP Joe Felsenstein's package of programs includes one of the earliest implementations of likelihood-based estimation of phylogeny. Incidentally, Felsenstein was also an early proponent of Bayesian estimation of phylogeny: Just read his 1968 Ph.D. Thesis!
  • MOLPHY A program by Jun Adachi and Masami Hasagewa that for a long time was the only game in town for maximum likelihood estimation of phylogeny using amino acid sequences.
  • PASSML A program by Pietro Lio that implements several models of amino acid change, including several Hidden Markov Models that can be used to predict secondary structure.

Other phylogeny programs:

  • An extensive list of phylogeny programs is available from Joe Felsenstein here.