[Bioperl-l] ClustalW Score?

Ryan Golhar golharam at umdnj.edu
Wed May 30 15:40:28 UTC 2007

How do I get the clustalw score from a clustalw alignment?  I'm using the
following code to align my sequences:

$aln_factory = Bio::Tools::Run::Alignment::Clustalw->new();

$seq[0] = ...
$seq[1] = ...
$seq[2] = ...
$seq[3] = ...

$aln = $aln_factory->align(\@seq);

I can get the percentage identity from the Bio::SimpleAlign object, but
there is no score.  I looked into it further and it doesn't look like the
score is being captured anywhere.  So, how does one get the score from
ClustalW using this method?


More information about the Bioperl-l mailing list