Dear Nicolai, I don’t have branch lengths, just the topology. Is there a way to estimate a posteriori the branch-lengths using molecular data for most, but not all species? In any way, I was aware of chronos function but I haven’t seen it used in the literature and wondered if there was any particular reason for that.
I will look into O’Meara’s package for the time being, Thanks to you and to Joseph for the reply, Fabio > On May 17, 2017, at 10:26, Nürk, Nicolai <nicolai.nu...@uni-bayreuth.de> > wrote: > > 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> >> <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 >> <mailto:R-sig-phylo@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> <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/
