[R] clustalW

[Jean lobry]

>  Hello,
>
>  I try to make directly with R a multiple alignment querying CLUSTAL W,
>  do you know how can I do this?
>
>  Thanks
>
>  Jérémy Mazet

See ?system on how to run an external program. There is an example
in the reverse.align() function from the seqinR package in which clustalW
can be run on the fly to align CDS at the amino-acid level:
http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/reverse.align.html

HTH,
-- 
Jean R. Lobry            (lobry at biomserv.univ-lyon1.fr)
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I,
43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE
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