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
_______________________________________________ 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/
