Re: [R-sig-phylo] Multiple sequence alignment in R?

2011-02-23 Thread Emmanuel Paradis 
The package phyloch has the functions mafft() and prank() which call the 
programs of the same name (two other MSA software):


http://www.christophheibl.de/Rpackages.html

phyloch has many other wrappers to system calls (mrbayes, raxml, ...) 
The package dna includes a port of ClustalW:


http://www.commanster.eu/rcode.html

Best,

Emmanuel

Nick Matzke wrote on 23/02/2011 07:21:

You can call any command-line thing from R with system().

Typically I use R to write the control file (e.g. for r8s), then do 
something like...


cmdstr = paste(program_name, -options, control_file,  
output.log, sep= )

system(cmdstr)

Cheers!
Nick

On 2/22/11 5:42 AM, Scott Chamberlain wrote:

Hello,


Is clustal multiple sequence alignment implemented in any R packages, 
or is there an easy way to call ClustalW on your hard drive from R, 
perhaps with system()



Sincerely,

Scott Chamberlain
Rice University, EEB Dept.

--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/

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[R-sig-phylo] Multiple sequence alignment in R?

2011-02-22 Thread Scott Chamberlain 
Hello, 


Is clustal multiple sequence alignment implemented in any R packages, or is 
there an easy way to call ClustalW on your hard drive from R, perhaps with 
system()


Sincerely, 

Scott Chamberlain
Rice University, EEB Dept.



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Re: [R-sig-phylo] Multiple sequence alignment in R?

2011-02-22 Thread Nick Matzke 

You can call any command-line thing from R with system().

Typically I use R to write the control file (e.g. for r8s), 
then do something like...


cmdstr = paste(program_name, -options, control_file, 
 output.log, sep= )

system(cmdstr)

Cheers!
Nick

On 2/22/11 5:42 AM, Scott Chamberlain wrote:

Hello,


Is clustal multiple sequence alignment implemented in any R packages, or is 
there an easy way to call ClustalW on your hard drive from R, perhaps with 
system()


Sincerely,

Scott Chamberlain
Rice University, EEB Dept.



[[alternative HTML version deleted]]

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--

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

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