[Seqinr-forum] Information!

[Leonor Palmeira]

Jeremias,

there is no built-in method to create alignments within the 'seqinr' 
package. These have to be run outside R and subsequently imported in R 
(for instance with the read.alignment() method).

If you are writing a script and don't want to leave R, you can run an 
alignment program by using the system() method.

For instance:

system("/usr/local/bin/clustalw -align -infile=inputfile.fasta 
-outfile=alignedfile.fasta -outorder=input -output=fasta -type=dna")

and then:

read.alignment("alignedfile.fasta",format="fasta")

Leo.

On 18/09/10 19:37, jeremias leao wrote:
> Dear friends,
>
> I have to make the alignment of genetic sequences of three species, but
> I can not do this in R. Could anyone help me, I have the sequences are
> in FASTA format.
>
> Regrards,
>
>
> Jeremias Leão.
>
>
>
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-- 
Leonor Palmeira, PhD

Phone: +32 4 366 42 69
Email: mlpalmeira AT ulg DOT ac DOT be
http://sites.google.com/site/leonorpalmeira

Immunology-Vaccinology, Bat. B43b
Faculty of Veterinary Medicine
Boulevard de Colonster, 20
University of Liege, B-4000 Liege (Sart-Tilman)
Belgium