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:
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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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:
