Re: [R-sig-phylo] estimating mutation rates
Thanks, guys. I just have a follow-up question: Does anyone know of a way to optimize BLs using optim.pml() while enforcing a molecular clock? Thanks! John On Thu, Nov 8, 2012 at 6:06 PM, Rob Lanfear rob.lanf...@gmail.com wrote: Hi John, Brian's suggestion is a good one. Another option would be to use any of a number of molecular dating programs (not strictly an R response, sorry) like R8S (for ML) or BEAST (for Bayesian). You can then specify your node dates and topology as constraints, and use the molecular data appropriately. The advantage of these approaches is that you'll have full control over the models of rate change, and over the treatment of uncertainty in the dates and rates (depending on which method you choose). However, if you really do believe your dates without question, and if your molecular dataset has sufficient power for rate estimates (i.e. at least a handful of substitutions estimated on each branch), I would just do as Brian suggested. Rob On 9 November 2012 06:35, Brian O'Meara bome...@utk.edu wrote: If you want the branch-specific substitution rate, you could estimate the branch lengths on a topology constrained to match the chronogram, then divide each of the molecular tree's branch lengths by the corresponding chronogram branch lengths to get these rates. If you want a global rate, you might constrain the molecular tree to have the same proportional branch lengths as the chronogram. Look at pml() in phangorn for calculating the likelihoods. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Thu, Nov 8, 2012 at 12:49 PM, john d dobzhan...@gmail.com wrote: Hi there, I have a well-supported phylogeny (with branch lengths proportional to absolute time) and I'm interested in estimating the mutation rate of an independently-obtained molecular dataset. Any suggestions? thanks! John ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Rob Lanfear Research Fellow, Ecology, Evolution, and Genetics, Research School of Biology, Australian National University www.robertlanfear.com July-September National Evolutionary Synthesis Center, 2024 W. Main Street, Suite A200, Durham, NC 27705-4667, USA phone: +1 919 668 4592 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] estimating mutation rates
Hi John, optim.pml has an parameter optRooted and you have to set it to TRUE. If you give the function an ultrametric tree it will optimise the edge lengths. Unfortunately it is not possible to use tree rearrangements with this option so far. Regards, Klaus On 11/9/12, john d dobzhan...@gmail.com wrote: Thanks, guys. I just have a follow-up question: Does anyone know of a way to optimize BLs using optim.pml() while enforcing a molecular clock? Thanks! John On Thu, Nov 8, 2012 at 6:06 PM, Rob Lanfear rob.lanf...@gmail.com wrote: Hi John, Brian's suggestion is a good one. Another option would be to use any of a number of molecular dating programs (not strictly an R response, sorry) like R8S (for ML) or BEAST (for Bayesian). You can then specify your node dates and topology as constraints, and use the molecular data appropriately. The advantage of these approaches is that you'll have full control over the models of rate change, and over the treatment of uncertainty in the dates and rates (depending on which method you choose). However, if you really do believe your dates without question, and if your molecular dataset has sufficient power for rate estimates (i.e. at least a handful of substitutions estimated on each branch), I would just do as Brian suggested. Rob On 9 November 2012 06:35, Brian O'Meara bome...@utk.edu wrote: If you want the branch-specific substitution rate, you could estimate the branch lengths on a topology constrained to match the chronogram, then divide each of the molecular tree's branch lengths by the corresponding chronogram branch lengths to get these rates. If you want a global rate, you might constrain the molecular tree to have the same proportional branch lengths as the chronogram. Look at pml() in phangorn for calculating the likelihoods. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Thu, Nov 8, 2012 at 12:49 PM, john d dobzhan...@gmail.com wrote: Hi there, I have a well-supported phylogeny (with branch lengths proportional to absolute time) and I'm interested in estimating the mutation rate of an independently-obtained molecular dataset. Any suggestions? thanks! John ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Rob Lanfear Research Fellow, Ecology, Evolution, and Genetics, Research School of Biology, Australian National University www.robertlanfear.com July-September National Evolutionary Synthesis Center, 2024 W. Main Street, Suite A200, Durham, NC 27705-4667, USA phone: +1 919 668 4592 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] estimating mutation rates
Hi there, I have a well-supported phylogeny (with branch lengths proportional to absolute time) and I'm interested in estimating the mutation rate of an independently-obtained molecular dataset. Any suggestions? thanks! John ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] estimating mutation rates
If you want the branch-specific substitution rate, you could estimate the branch lengths on a topology constrained to match the chronogram, then divide each of the molecular tree's branch lengths by the corresponding chronogram branch lengths to get these rates. If you want a global rate, you might constrain the molecular tree to have the same proportional branch lengths as the chronogram. Look at pml() in phangorn for calculating the likelihoods. Best, Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Thu, Nov 8, 2012 at 12:49 PM, john d dobzhan...@gmail.com wrote: Hi there, I have a well-supported phylogeny (with branch lengths proportional to absolute time) and I'm interested in estimating the mutation rate of an independently-obtained molecular dataset. Any suggestions? thanks! John ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
