Hello, Marc Suchard has recently implemented this in the package epibase - check the function read.annotated.nexus.
All the best Thibaut. ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Tom Diggs [jtdi...@mail.ad.uab.edu] Sent: 19 June 2013 18:33 To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Difficulty getting posterior probabilities into ape? Hi all, I was wondering if anyone else has had this problem, and how they addressed it. I've been using BEAST to generate trees, and TreeAnnotator to summarize them. In the output nexus file, the tree plainly has posterior probabilities for each node listed, but when I try to import the trees into R, my tree has no node labels (mytree$node.labels = NULL). I searched the archives for this listserve, and found one instance of this problem cropping up with MrBayes output. http://www.mail-archive.com/r-sig-phylo@r-project.org/msg02227.html Unfortunately, the package "phybase", listed as a potential solution to the problem, is no longer in CRAN. Am I missing something obvious? Is ape having trouble reading the node labels for some reason? Any help would be much appreciated. Thanks so much. Tom [[alternative HTML version deleted]] _______________________________________________ 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/ _______________________________________________ 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/