[R-sig-phylo] chronoMPL/APE
The "strange" shape of your tree seems to result from negative branch lengths. If your goal is to just obtain an ultrametric tree under no specific assumptions, use compute.brtime (yourtree, method="coalescent", force.positive=TRUE). Where 'yourtree' must be an object of class phylo. force.positive=TRUE will prevent negative branch lengths to occur in your tree. I hope this helps. Juan A. Balbuena -- Dr. Juan A. Balbuena Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia http://www.uv.es/~balbuena P.O. Box 22085 http://www.uv.es/cophylpaco 46071 Valencia, Spain e-mail: j.a.balbu...@uv.es tel. +34 963 543 658 fax +34 963 543 733 NOTE! For shipments by EXPRESS COURIER use the following street address: C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain. ___ 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] chronoMPL/APE
Dear all, I just started to work with R and I have the following problem: I calculated a phylogenetic tree in RAmML. For further analysis, I need an ultrametric tree which I wanted to make with the chronoMPL command in APE. However, the tree was not dichotomous and I used the multi2di(phylogeny, random = TRUE) function to resolve the polytomies. Then I used the chronoMPL function chronoMPL(phy, se = TRUE, test = TRUE) to make the tree ultrametric. However, the ultrametric tree looks really strange (see attachment). Do you have any suggestion? Thank you in advance, Jacqueline test.pdf Description: Adobe PDF document ___ 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/
