Re: [R-sig-phylo] Chronos function in ape
Hi Marco, chronos uses specific models for the variation in substitution rates among branches and I'm not sure whether these models apply to your data. Maybe you can use chronos with model = "clock" if you can assume that drift is constant throughout your tree. HTH Emmanuel Le 06/07/2016 19:02, Marco Fracassetti a écrit : Hi to all of you, I want to calibrated a relationship tree done with Treemix (Pickrell & Pritchard 2012) done with SNPs frequency. The branch length of the tree reflect the amount of genetic drift. The chronos function from the package ape want tree whose branch lengths are in number of substitution per sites. Is It correct to t use the chronos function ? There is another R function that could transform a relationship tree in ultrametric tree? Thanks in advance for the help, Marco [[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/4088P9JAzi9 ___ 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/
Re: [R-sig-phylo] Chronos function in ape
Geiger has congruify functions that can use pathd8 to make a tree ultrametric (perhaps using an external chronogram to date it). There's some code in there to use r8s, as well, but it takes some digging. Best, Brian ___ Brian O'Meara Associate Professor Dept. of Ecology & Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info On Wed, Jul 6, 2016 at 1:02 PM, Marco Fracassetti < marco.fracasse...@unibas.ch> wrote: > Hi to all of you, > > I want to calibrated a relationship tree done with Treemix (Pickrell & > Pritchard 2012) done with SNPs frequency. The branch length of the tree > reflect the amount of genetic drift. > The chronos function from the package ape want tree whose branch lengths > are in number of substitution per sites. > Is It correct to t use the chronos function ? > There is another R function that could transform a relationship tree in > ultrametric tree? > > Thanks in advance for the help, > > Marco > > [[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/
Re: [R-sig-phylo] chronos function
Hi Francisca, The scale of the branch lengths of the chronogram should be defined by the calibration points provided to chronos(). Maybe you used the default (age = 1 at the root) so that the branch lengths are (logically) all less than one. Best, Emmanuel Le 06/05/2015 15:40, Francisca Cunha Almeida a écrit : Dear all, I am trying to make ultrametric trees from a ML tree. The chronos function runs all right, but the scale of the calibrated tree I get does not reflect the calibration I used; instead it seems to be still in substitutions per site. Is it what I should expect? Thanks in advance, Francisca ___ 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/
Re: [R-sig-phylo] chronos function
Hi Fabricia, This error apparently happens when the root age is unknown and must be estimated with other parameters. A fixed version of the function can be found on ape's web site: http://ape-package.ird.fr/ Best, Emmanuel Le 09/04/2014 17:28, Fabricia Nascimento a écrit : Hi, I am analyzing lots of trees in which I need it to be ultrametric. I decided to use the function chronos, but in the middle of my run I got the following error message which I don't know the meaning: Error in nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) : NA/NaN gradient evaluation Someone has previously notice a similar error but I could not find a reply associated to the question (http://www.mail-archive.com/r-sig-phylo@r-project.org/msg03208.html) Thanks very much, Fabricia. [[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/ ___ 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/
