[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?

Ryan





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