Just to add to Juan's comment, for most analyses where you need branch lengths, you need them to be fairly accurate (but not all, so his is useful advice for those cases). In cases where you do need good branch lengths (diversification, ancestral state reconstruction, phylogenetic diversity, rates of evolution, many others), doing chronopl() with constraints or using congruify.phylo() in geiger using a reference chronogram could be useful. This may also be a case where one would leave our happy R ecosystem (or use a system() call to quietly leave) to use BEAST, RevBayes, r8s, treePL, or similar.
Best, Brian _______________________________________________________________________ Brian O'Meara, http://www.brianomeara.info, especially Calendar <http://brianomeara.info/calendars/omeara/>, CV <http://brianomeara.info/cv/>, and Feedback <http://brianomeara.info/teaching/feedback/> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville Associate Director for Postdoctoral Activities, National Institute for Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS) Communication Director, Society of Systematic Biologists On Tue, Jan 17, 2017 at 9:13 AM, Juan Antonio Balbuena <j.a.balbu...@uv.es> wrote: > 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 > <http://www.uv.es/cavanilles/zoomarin/index.htm> > 46071 Valencia, Spain > e-mail: j.a.balbu...@uv.es tel. +34 963 543 658 > <+34%20963%2054%2036%2058> fax +34 963 543 733 > <+34%20963%2054%2037%2033> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > *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-ph...@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/
