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.
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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
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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
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"[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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