Dear Emmanuel, Thank you very much for your response. I cannot see how to provide the substitution rate to the phangorn::pml_bb() function, but I was looking at the ape::node.dating() function and it appears that I could provide the substitution rate to the "mu" argument and then set the "node.dates" argument to NA or zero for all tips (I'm not sure if NA or zero would be preferable to force the tips to all be from a single time point). Do you think that would work? I'm not sure how to make ape::node.dating() accept a substitution rate rather than try to estimate one. Maybe an option could be added to allow mu to equal a user-specified number rather than the output of ape::estimate.mu()?
Another option might be to calculate an estimated age for every node connecting sister taxa in the tree by converting the genetic distances between sister pairs to divergence times using the substitution rate and then use those as priors in ape::chronos(). I suppose I could also apply that logic to date all of the nodes by using the mean pairwise distances between taxa on either side of a node and converting that to divergence times (although the R code for such a calculation would likely take me a while to figure out). Would that be another option? Thanks again, Vincenzo On Sat, Mar 2, 2024 at 5:44 AM Emmanuel Paradis <emmanuel.para...@ird.fr> wrote: > 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/ > [[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/
