[Bioperl-l] Consensus with ClustalW

FERNANDA SCARIOT fe.scariot at cttmar.univali.br
Mon Jun 7 17:45:28 EDT 2004

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  
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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