[Bioperl-l] Bio::Align::AlignI for EMBOSS:needle

Ryan Golhar golharam at umdnj.edu
Mon Aug 15 11:38:46 EDT 2005

EMBOSS needle reports percent identity and percent similarity, however
Bio::Align::AlignI has no method for obtain the percent similarity.  

My code is essentially:

my $in = new Bio::AlignIO(-format => 'emboss', -fh => new
my $aln = $in->next_aln;
$fepct = $aln->overall_percentage_identity;

I tried the different percentage_identity methods to see if any of them
work, but they don't give the similarity number.  Is there a way to get
the percent similarity through bioperl?

Also, the description part of the document for
overall_percentage_identity has a type for the Title.


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