Dear Klaus & Emmanuel, Thank you for your fast answers. Both work!There still is a deviation at the level of the consensus tree from Phylip, but my technical problem has been solved.
Best wishes,
Thomas
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# the script below uses the list of trees ("example_trees.tre") from
# http://evolution.genetics.washington.edu/phylip/doc/consense.htmltr=read.tree(file="example_trees.tre") ct=consensus(tr,p=0.5) sv=prop.clades(ct,tr) # using phangorn library(phangorn) # adds support values as node.label ct=plotBS(ct, tr) plot(ct,show.node.label=TRUE, type="phylogram") nodelabels(sv,frame="none", adj=c(-1,-1),col="red") ========================= On 12/16/13 16:37, Emmanuel Paradis wrote:
Hi Thomas, Have you tried prop.clades? Best, Emmanuel -----Original Message----- From: Thomas Manke <ma...@ie-freiburg.mpg.de> Sender: r-sig-phylo-boun...@r-project.org Date: Mon, 16 Dec 2013 11:52:33 To: <r-sig-phylo@r-project.org> Subject: [R-sig-phylo] plotting support value Dear Forum, I have a list containing sampled trees for the same "taxa" and would like to plot their consensus tree with the support values (absolute numbers or frequencies) for the various branches. (as done by the Consense program of the Phylip suite) I understand that boot.phylo() returns an object "bs" that contains such information as bs$BP. My scenario is similar, but the sampled trees are not based on sequence information and boot.phylo() is not applicable here. I assume the support values can be obtained from prop.part(), but I could not figure how. Thank you for any help or suggestions, Thomas #tr is list of trees ct<-consensus(tr, p=0.5) # majority consensus pt<-prop.part(tr) pc<-prop.part(ct) # calculate support values sv <- f(pc, pt) = ??? plot(ct); nodelabels(sv) _______________________________________________ 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/
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