Re: [R-sig-phylo] Plotting Posterior Probabilities from MrBayes Trees (An Update)

Hi all, here is a small function which it is very similar to David's 2nd script, but it is a bit more compact: library(phangorn) # requires the newest pangorn version >= 1.99-8 addConfidences.phylo <- function(to, from){ conf = attr(addConfidences(as.splits(to), from), "confidences") nTips

Re: [R-sig-phylo] Plotting Posterior Probabilities from MrBayes Trees (An Update)

Hello all, Unable to get phyloch's read.mrbayes() to read my .con.tre files (for reasons unknown), I've gone with Graham's suggestion to use the simple output format from sumt. However, as I have a large number of analyses which took considerable computational time (and I am stubborn to learn how

Re: [R-sig-phylo] tip order in phylogeny - How does it work?

Look at reorder.phylo() in ape and reorder() in phylo4: your desired tip order may be there. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Postdoc collaborators

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[R-sig-phylo] tip order in phylogeny - How does it work?

Hello I am working on a simulation that requires adding a number of random tips to multiple phylogenies: treeP <- read.nexus(file= "my file.tre") # 5K trees used to build a consensus tree (treeP is thus a multiPhylo object) NT = 30 # number of taxa in phylogeny