Emmanuel Paradis wrote: > If you are Bayesian, the trees sampled from an MCMC are here for estimation > including of the branch lengths, so you use them to compute some sort of > consensus topology as well as its branch lengths. So it makes sense that > MrBayes can do a consensus tree with branch lengths.
I endorse the rest of Emmanuel's advice but let me quibble with this one. The posterior on trees may not consist mostly of trees varying around a single consensus. If the posterior had, for example, two modes, each centered around a different tree, a single consensus tree might not be appropriate, and branch lengths computed by averaging lengths over the two modes might not be a good guide to what the trees in the posterior looked like. I don't know enough about MrBayes features to know whether they have some way around this. There is a similar issue with parsimony methods -- the set of most parsimonious trees may have a consensus, which may well not be a most parsimonious tree. People who see the consensus of most parsimonious trees may not realize that the particular tree they are looking at is not most parsimonious. J.F. ---- Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA (from 1 October 2012 to 10 December 2012 on sabbatical leave at) Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, CA 94710 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
