Hi Nick, I tried nj, but the topology I obtain from that is totally different. I am not sure if it has anything to do with the fact that the tree was created based on maximum likelihood? Thanks though!
Meche On Thu, May 12, 2011 at 4:23 PM, Nick Matzke <mat...@berkeley.edu> wrote: > The APE command NJ (neighbor-joining) will form a tree from a distance > matrix, so that's one option. You could do it and then see if you get the > same topology from NJ as from your topology tree. The branch lengths will > reflect whatever distances were calculated from the data (which might be one > of several corrected or uncorrected distances, depending on the input > sequence/character data). > > Cheers, > Nick > > On 5/12/11 2:18 PM, mgavil2 wrote: >> >> All, >> I have a tree topology (tree_name.tre), and a distance matrix, based >> on that tree topology. However I cant not seem to find the nexus file >> from which the matrix was generated. Is there a way to use that >> distance matrix to incorporate branch lengths into my topology? >> I have looked into all the threads of questions posted in the list, >> but still can not find an answer. my final objective is just to >> generate a tree with branch lengths proportional to the distances on >> the matrix (reviewers requirement for a publication). >> >> Any suggestions would be greatly appreciated! >> >> Thanks. >> >> Maria Mercedes >> > > -- > ==================================================== > Nicholas J. Matzke > Ph.D. Candidate, Graduate Student Researcher > > Huelsenbeck Lab > Center for Theoretical Evolutionary Genomics > 4151 VLSB (Valley Life Sciences Building) > Department of Integrative Biology > University of California, Berkeley > > Graduate Student Instructor, IB200B > Principles of Phylogenetics: Ecology and Evolution > http://ib.berkeley.edu/courses/ib200b/ > http://phylo.wikidot.com/ > > > Lab websites: > http://ib.berkeley.edu/people/lab_detail.php?lab=54 > http://fisher.berkeley.edu/cteg/hlab.html > Dept. personal page: > http://ib.berkeley.edu/people/students/person_detail.php?person=370 > Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html > Lab phone: 510-643-6299 > Dept. fax: 510-643-6264 > > Cell phone: 510-301-0179 > Email: mat...@berkeley.edu > > Mailing address: > Department of Integrative Biology > 3060 VLSB #3140 > Berkeley, CA 94720-3140 > > ----------------------------------------------------- > "[W]hen people thought the earth was flat, they were wrong. When people > thought the earth was spherical, they were wrong. But if you think that > thinking the earth is spherical is just as wrong as thinking the earth is > flat, then your view is wronger than both of them put together." > > Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, > 14(1), 35-44. Fall 1989. > http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm > ==================================================== > -- Maria Mercedes Gavilanez Department of Biological Sciences 107 Life Sciences Building Louisiana State University Baton Rouge, LA 70803 (225)578-4284 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
