Hi Vincenzo, There's no direct way to do this with ape::chronos(). You may have a look at the function phangorn::pml_bb() but I'm not sure it can estimate the dates if the rate is provided in a model object given as main argument(?)
That said, I expect that estimating so many dates to be very challenging (unless you have a lot of known dates for calibration). This implies that you are certainly right to look for an approach where you don't need to estimate the rates. Best, Emmanuel ----- Le 27 Fév 24, à 22:40, Vincenzo Ellis vael...@udel.edu a écrit : > Dear R-sig-phylo members, > > I've made a maximum likelihood tree in Raxml for several thousand taxa > using a single gene that has an estimated substitution rate of 0.006 > substitutions/nucleotide/My. Is there a way to use chronos in ape to apply > that substitution rate as a fixed clock rate and generate an ultrametric > time-scaled version of the tree? > > Thank you, > > Vincenzo > > [[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/
