Dear Vincenzo, For ML estimates the edge length are the expected number of substitutions per site, which depends on the product of rate and time. So you need either a rate estimate or calibration points to estimate the time. If you divide the edge length by the rate the edges should be proportional to time. With pml_bb you can estimate ultrametric or tip dated trees with a strict molecular clock model. Kind regards, Klaus
Von meinem iPhone gesendet > Am 04.03.2024 um 21:06 schrieb Vincenzo Ellis <vael...@udel.edu>: > > Dear Liam, > > Thank you for your answer. Yes, I have a hypothesized average clock rate > and no explicit calibration points. > > If I use ape::chronos() with default values it gives me a depth of 1 at the > root. So I suppose to rescale the branch lengths I just need to multiply > all of the branch lengths by a value (i.e., tree$edge.length * value), is > that right? > > Thanks again, > > Vincenzo > >> On Mon, Mar 4, 2024 at 11:43 AM Liam J. Revell <liam.rev...@umb.edu> wrote: >> >> Dear Vincenzo. >> >> If I understand your problem problem, you do not have any explicit >> calibration points -- but you have a hypothesized average clock rate? >> >> If so, then you can obtain an ultrametric tree from* ape::chronos* for >> any value of the smoothing parameter (*lambda*) and then simply re-scale >> it to have the desired total depth (based on your hypothesized clock rate). >> >> To choose a "correct" value of *lambda* one can use cross-validation as >> described in Sanderson (2002; doi:10.1093/oxfordjournals.molbev.a003974). >> >> Others should feel welcome to weigh in if this is not right. >> >> All the best, Liam >> Liam J. Revell >> Professor of Biology, University of Massachusetts Boston >> Web: http://faculty.umb.edu/liam.revell/ >> Book: Phylogenetic Comparative Methods in R >> <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> >> (*Princeton University Press*, 2022) >> >> >> On 3/4/2024 11:09 AM, Vincenzo Ellis wrote: >> >> [You don't often get email from vael...@udel.edu. Learn why this is >> important at https://aka.ms/LearnAboutSenderIdentification ] >> >> CAUTION: EXTERNAL SENDER >> >> 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> >> <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.orghttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193183565%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=wV2IJEHNPpbc2a7Erg%2F14jVmDcIqLshVohWaKa6vG6U%3D&reserved=0 >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at >> >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193196126%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=d4fLpFetiQDBjHKTmdlDijgx%2F360Z2oPddHLdCqrrUQ%3D&reserved=0 >> <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.orghttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193201324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=XV4ICgm3xswIObonT8pYZcEHsQVSImxPcKHqefo8zuk%3D&reserved=0 >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193205831%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=dbdnzYPubwMiyqGLncCCl8P5bPDQ%2Bn3QPUUEAt4sQZQ%3D&reserved=0 >> <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/ _______________________________________________ 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/
