Re: [R-sig-phylo] Show Informative Sites?
Leandro Jones -- 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 disagree. If the only way you can interpret anything is by parsimony, sure. But for statistical phylogenetics, it has information. It works against any phylogeny that has all its branch lengths short, for example. Eliminating that character, not telling the statistical method you did that, and then going ahead with the analysis is a Big Mistake. J.F. Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Show Informative Sites?
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
Re: [R-sig-phylo] Show Informative Sites?
Date: Sat, 17 Sep 2011 11:21:45 -0700 From: Jimmy O'Donnell jodonn...@biology.ucsc.edu To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Show Informative Sites? Message-ID: f1a6d774-e4e2-4903-b959-61cb33612...@biology.ucsc.edu Content-Type: text/plain; charset=us-ascii 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? The function seg.sites() in ape tells you which sites are polymorphic in a DNAbin object ?seg.sites HTH Sam 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 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Show Informative Sites?
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
Re: [R-sig-phylo] Show Informative Sites?
Nick Matzke wrote: All sites are informative under likelihood, ... and under Bayesian methods, and under distance matrix methods too. If you leave out uninformative sites without compensating for doing that by an explicit statistical correction, you will have some very unpleasant surprises. J.F. Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
