[R-sig-phylo] Show Informative Sites?

Nick Matzke matzke at berkeley.edu
Tue Sep 20 05:49:15 CEST 2011


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<matzke at 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
>>> jodonnell at biology.ucsc.edu
>>> (407)744-3377
>>>
>>> _______________________________________________
>>> R-sig-phylo mailing list
>>> R-sig-phylo at 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: matzke at 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 at 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: matzke at 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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