Liam, I am pretty sure it is the correct distance matrix, but I ll look again to make sure . Also looking at the topology (even though it is unrooted, it looks pretty off. I mean i find species from one clade within a (many) different clades?
Also, I ran your code for finding the optimum tree based on least squares, and I have a few questions about my outcome: 1. what is a "good" Q score? mine said it is 0.0422062959681288 found after 19 nearest neighbor interchange(s). is this right? I mean it find one so fast for the example you sent, but the value is also so different. 2. based on what you said, the distance matrix I obtain from the new LStree should exactly resemble the distance matrix I used to generate the tree right? however, this does not happen in my case, the original distance matrix is different from the distance matrix generated from the LStree. Any ideas why this might be happening? I am trying to run the same procedure with a different tree (from which I am sure I have the distance matrix), to see if it is that my matrix doesn't belong to the topology i give it, but keep getting an error saying "Error in solve.default(t(X) %*% X) : Lapack routine dgesv: system is exactly singular" Maybe because that tree is ultrametric? 3. Also, the tree I get from NJ and the tree I get fromt he optimum LS is different too, as are the distance matrices? should these two be the same? Sorry for all the questions! Meche On Thu, May 12, 2011 at 5:33 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > Hi Nick & al. > > Actually, Nick's method should work too. > > If the distance matrix is a patristic distance matrix based on the ML tree, > then neighbor-joining ought to recover the exact topology and branch lengths > of your ML tree. This is on p. 166 of Felsenstein (2004): > "Neighbor-joining, like the least squares methods, is guaranteed to recover > the true tree if the distance matrix happens to be an exact reflection of a > tree." > > Maria, are you sure that your distance matrix came from the branch lengths > in your ML tree; and, furthermore, are you sure that NJ did not give you the > correct tree? Keep in mind that NJ will return an unrooted tree and that > the branches might be rotated around any node (thus, your plotted tree may > seem quite different from the ML tree). > > - Liam > > -- > Liam J. Revell > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://phytools.blogspot.com > > On 5/12/2011 5:28 PM, mgavil2 wrote: >> >> 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
