[Bioperl-l] Consensus with ClustalW

[Jason Stajich]

I assume this is DNA?
This should work:
 my $consensus = $a->consensus_iupac();

-jason
On Mon, 7 Jun 2004, FERNANDA SCARIOT wrote:

> Hi...
>
> I'm new in BioPerl...
> I need a help with multiple alignment. I'm using ClustalW to do the alignment,
> but I need to make a DEGENERATE consensus sequence.
>
> I'm using: "$factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);"
>
> When I use "$aln->consensus_string()", it makes a consensus without
> degenerations. I already used "$aln->match_line ();", but it doesn't do what I
> want.
>
> Thanks for the help in advance,
> Fernanda Scariot.
>
> Laboratório de Sistemas Embarcados e Distribuídos
> Ciência da Computação
> Univali - Itajaí - SC - Brazil
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu