Hi all, It can be done with phyloch but I forgot the name of the function.
HTH Emmanuel -----Original Message----- From: Leandro Jones <lrj...@gmail.com> Sender: r-sig-phylo-boun...@r-project.org Date: Mon, 19 Sep 2011 07:35:32 To: <r-sig-phylo@r-project.org> Subject: [R-sig-phylo] Show Informative Sites? Nick´s rules won´t allways work in a Parsimony context. For example, a position like this one: 1 A 2 A 3 T 4 C would be "informative" under rules (a) and (b), but it is in reality uninformative, as any of the possible trees have a length of 2. Thus, this character tells us nothing about _phylogeny_. I don´t know of any R function capable of solving Jimmy´s problem, but I would suggest using TNT. TNT implements a function (isinfo) that tells you if a given character is or is not informative. Hope this helps. Leandro 2011/9/17 Nick Matzke <mat...@berkeley.edu>: > All sites are informative under likelihood, but I assume you mean > parsimony-informative, in which case all you have to do is count which sites > are either (a) uniform or (b) uniform except for differences found only in a > single species. > > Probably easiest if you convert the read.nexus.data output to a dataframe > with as.data.frame, then use unique and == to count the number of states in > each site... > > > On 9/17/11 11:21 AM, Jimmy O'Donnell wrote: >> >> Hi all, >> >> A simple question to which I can't seem to find an answer: is there a way >> to show only the informative sites of a DNA sequence dataset in R? >> >> Thanks, >> >> Jimmy >> -- >> Jimmy O'Donnell >> PhD Candidate >> Ecology and Evolutionary Biology >> University of California >> Santa Cruz, CA 95060 >> jodonn...@biology.ucsc.edu >> (407)744-3377 >> >> _______________________________________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > > -- > ==================================================== > 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 > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Leandro R. Jones, Ph.D. -- Leandro R. Jones, Ph.D. _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
