Dear Fabio, you might also use the chronos function in ape, which demands a data frame with calibrations (if you have information from published trees that could be use to calibrate your tree; cf. email from Joe), and which assumes that you have a phylogenetic tree whose branch lengths are in number of substitution per sites.
library(ape) #make calibration df (interactive: you can click on a node on the tree and specify the min/max age) cal <- makeChronosCalib(your.phy, node = "root", age.min = 1, age.max = age.min, interactive = TRUE, soft.bounds = FALSE) #calculate the chronogram e.g. using a strict clock model (better check ?chronos) phy.ultra <- chronos(your.phy, lambda = 1, model = "correlated", calibration = cal) HTH, nmn --- Dr. Nicolai M. Nürk Institute of Plant Systematics Department of Biology University of Bayreuth Universitätsstraße 30 95447 Bayreuth On 17 May 2017, at 14:26, Joseph W. Brown wrote: Fabio you might have luck with Brian O'Meara's datelife: https://github.com/phylotastic/datelife <https://github.com/phylotastic/datelife> Essentially it grabs dates from published trees and applies it to your own. Brian can provide more details. (^_<)〜☆ HTH. JWB ________________________________________ Joseph W. Brown Post-doctoral Researcher, Smith Laboratory University of Michigan Department of Ecology & Evolutionary Biology Room 2071, Kraus Natural Sciences Building Ann Arbor MI 48109-1079 josep...@umich.edu<mailto:josep...@umich.edu> On 17 May, 2017, at 08:12, Fábio Machado <macfa...@gmail.com> wrote: Dear community, I was wondering if there is any methodology implemented in R to date cladograms, either using only the tree topology or using additional molecular data. If not, what would be the best solution to obtain a dated phylogeny, given that I have only a tree topology to work with. Best regards, Fabio Andrade Machado Becario Postdoctoral - CONICET Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” División de Mastozoología, Buenos Aires, Av. Ángel Gallardo 470 (C1405DJR) Argentina f.mach...@usp.br <mailto:f.mach...@usp.br> ; macfa...@gmail.com <mailto:macfa...@gmail.com> +55 11 982631029 skype: fabio_a_machado Lattes: http://lattes.cnpq.br/3673327633303737 <http://lattes.cnpq.br/3673327633303737> Google Scholar: http://scholar.google.com/citations?hl=en&user=2l6-VrQAAAAJ <http://scholar.google.com/citations?hl=en&user=2l6-VrQAAAAJ> [[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/ [[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/
