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MrBayes is a program for the Bayesian estimation of phylogeny.


  • John Huelsenbeck
  • Fredrik Ronquist

Summarizing Samples of Substitution Model Parameters

During the run, samples of the substituion model parameters have been written to the .p files every samplefreq generation. These files are tab-delimited text files.

The columns contain:

  1. Gen: the generation number
  2. LnL: the log likelihood of the cold chain
  3. TL: the total tree length (the sum of all branch lengths)
  4. r(A<->C), r(A<->G), etc: the six GTR rate parameters
  5. pi(A), pi(C), etc: the four stationary nucleotide frequencies
  6. alpha: the shape parameter of the gamma distribution of rate variation
  7. pinvar: the proportion of invariable sites.

MrBayes tree file scanners

Torsten Eriksson of the Bergius Botanical Garden, Stockholm, Sweden (torsten AT bergianska DOT se) makes available MrBayes tree file scanners. These are two Perl scripts that scan the output parameter files produced by MrBayes (versions 2.01 and 3). One saves the tree corresponding to the best sample. The other saves all trees that contain a specific node (a specific grouping).

scans an output parameter file (".p") for the best sample(s) and puts the corresponding tree(s) in a separate NEXUS tree file.
scans an output tree file (".t") and selects only those trees which contain a specified node.

They are distributed together, and available from his software distribution site:


See also


  • Ronquist F and Huelsenbeck JP (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
  • Huelsenbeck JP and Ronquist F (2001). MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.

External links

Topics in phylogenetics
Relevant fields: phylogenetics | computational phylogenetics | molecular phylogeny | cladistics
Basic concepts: synapomorphy | phylogenetic tree | phylogenetic network | long branch attraction
Phylogeny inference methods: maximum parsimony | maximum likelihood | neighbour joining | UPGMA