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
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University of California, Berkeley
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Principles of Phylogenetics: Ecology and Evolution
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http://phylo.wikidot.com/
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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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