Re: [R] clustalW

From: Jean lobry <lobry_at_biomserv.univ-lyon1.fr>
Date: Sun, 17 Jun 2007 18:19:41 +0200

> 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
allo  : +33 472 43 27 56     fax    : +33 472 43 13 88
http://pbil.univ-lyon1.fr/members/lobry/

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Received on Sun 17 Jun 2007 - 16:24:47 GMT

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