Re: [R-sig-phylo] Show Informative Sites?
That's what I meant with (b), but it was perhaps too hastily written... On 9/18/11 5:41 PM, Leandro Jones wrote: 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: 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 -- 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?
Hi all, It can be done with phyloch but I forgot the name of the function. HTH Emmanuel -Original Message- From: Leandro Jones Sender: r-sig-phylo-boun...@r-project.org Date: Mon, 19 Sep 2011 07:35:32 To: 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 : > 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
[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 : > 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
