I typically use a non-R tool like treeannotator (from the BEAST package) to do this type of thing, especially when involving large numbers of big trees.
HTH. Joseph. On Wed, Jan 23, 2019 at 4:42 PM Alina van dijk <alinavd...@gmail.com> wrote: > Hi everyone, > > My name is Alina, I'm attending master degree in ecology and I have a > little problem with my consensus phylogeny. I used 1000 phylogeny of > birdtree to construct the consensus tree but now I need to insert the dates > in this consensus tree. > > To accomplish this idea, I tried different methods: > consensustree<-averageTree > (tree,method="symmetric.difference") but the result is a consensus tree in > topology, binary and rooted but not ultrametric. For this problem I used > consensus_tree_ultrametric > <-compute.brlen(consensustree,method="Grafen",power=1), but the edge > lengths was altered. > > So, I used another method to make a consensus tree using phytools > consensustree_another_method <- consensus.edges(multiphylo,method = > "mean.edge") as a result, a ultrametric tree, rooted with consensus edges > lengths, but have polytomies :( > > I also tried using phylobase , proposed by Brian O'Meara in this link: > > https://grokbase.com/t/r/r-sig-phylo/12bn9x5gv4/why-no-branch-lengths-on-consensus-trees > , > but as a result, my consensus tree wasn´t ultrametric and the > transformation also altered the edge lengths. > > I only need to insert the dates based on the trees dated by Jetz in this > consensus tree and as result, an ultrametric tree, with consensus edges > lengths and no polytomy. > > Does anyone know how to solve that problem? > > Thanks in advance, > Best Regards, > > Alina > > [[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/ > [[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/
