Hi everyone, Thanks Emmanuel and Joseph for sharing your thoughts! Emmanuel, today I tried multi2di and it works. But, if I understand correctly, this function transforms the dichotomies with branches of length zero. So for me, in fact, doesn't solve the politomy. Right? Joseph, I'm only a begginer with R and this program already gives me a lot of headache. It drives me crazy think in another program... hahahha Just kidding! :) But, nice to know that I have a plan B! I will take a look!
Thanks in advance, Best Regards, Alina Em qua, 23 de jan de 2019 às 16:29, Emmanuel Paradis < emmanuel.para...@ird.fr> escreveu: > Hi Alina, > > Did you try multi2di() to remove polytomies? > > Best, > > Emmanuel > > Le 23/01/2019 à 17:41, Alina van dijk a écrit : > > 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/ > > > > > > Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : > http://f.security-mail.net/VKQxzoa2 > > > > > [[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/
