Difference between revisions of "MrBayes"
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* [[John Huelsenbeck]] | * [[John Huelsenbeck]] | ||
* [[Fredrik Ronquist]] | * [[Fredrik Ronquist]] | ||
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| + | == Summarizing Samples of Substitution Model Parameters == | ||
| + | |||
| + | During the run, samples of the '''substituion model parameters''' have been written to the .p files every <tt>samplefreq</tt> generation. These files are tab-delimited text files. | ||
| + | |||
| + | The columns contain: | ||
| + | # <tt>Gen</tt>: the generation number | ||
| + | # <tt>LnL</tt>: the '''[[Likelihood-ratio test|log likelihood]]''' of the '''cold chain''' | ||
| + | # <tt>TL</tt>: the total tree length (the sum of all branch lengths) | ||
| + | # <tt>r(A<->C)</tt>, <tt>r(A<->G)</tt>, etc: the six '''[[GTR]] rate parameters''' | ||
| + | # <tt>pi(A)</tt>, <tt>pi(C)</tt>, etc: the four '''stationary nucleotide frequencies''' | ||
| + | # <tt>alpha</tt>: the shape parameter of the [[Gamma distribution|gamma distribution]] of rate variation | ||
| + | # <tt>pinvar</tt>: the proportion of invariable sites. | ||
== MrBayes tree file scanners == | == MrBayes tree file scanners == | ||
Revision as of 17:05, 3 January 2006
MrBayes is a program for the Bayesian estimation of phylogeny.
Contents
People
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:
- Gen: the generation number
- LnL: the log likelihood of the cold chain
- TL: the total tree length (the sum of all branch lengths)
- r(A<->C), r(A<->G), etc: the six GTR rate parameters
- pi(A), pi(C), etc: the four stationary nucleotide frequencies
- alpha: the shape parameter of the gamma distribution of rate variation
- 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).
- mbscan
- scans an output parameter file (".p") for the best sample(s) and puts the corresponding tree(s) in a separate NEXUS tree file.
- treefilter
- 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: http://www.bergianska.se/index_forskning_soft.html.
Resources
-
Bayesian Analysis of Molecular Evolution using MrBayes — by Huelsenbeck JP and Ronquist F.
See also
References
- 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
- MrBayes: Bayesian Inference of Phylogeny — official Homepage
- MrBayes Wiki — ('Christoph')
