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://w
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 Chamberl
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]]
__
