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
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Nicholas J. Matzke
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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:
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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
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Leandro R. Jones, Ph.D.
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