John, I had to double-check this with someone who knew better first, but they confirmed for me that the answer is that MrBayes doesn't infer a Q matrix. By default, the Q matrix for Mk in MrBayes is always held fixed so the rates of transition are always equal and fully reversible, i.e. a simple Jukes-Cantor model. There's no setting that allows MrBayes to freely vary and infer a Q matrix, but you can relax the assumption of symmetrry via the symmetric Dirichlet hyperprior. If you want to infer a Q model under a different model, there are lots of R functions for fitting models to discrete character data, such as in geiger or ape.
I suggest seeing April Wright et al.'s recent paper in Systematic Biology for a clear explanation of this:. http://sysbio.oxfordjournals.org/content/65/4/602 I hope this helps! Cheers, -Dave Bapst On Tue, Jul 19, 2016 at 3:15 PM, John Denton <jden...@amnh.org> wrote: > Hi folks, > > I need to do some simulation using the Mkv model, and am wondering if there > is a way to extract Mk Q-matrix values from mrbayes. A look at report lists > revmat as an output, but I do not see any parameters in the .p files when I > finish the run. > > Thanks, > > ~John > > > John S. S. Denton, Ph.D. > Department of Vertebrate Paleontology > American Museum of Natural History > www.johnssdenton.com > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/