The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.


Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments


  use strict;
  my $stats = Bio::Align::PairwiseStatistics->new();

  # get alignment object of two sequences somehow
  my $pwaln;
  print $stats->number_of_comparable_bases($pwaln);
  my $score = $stats->score_nuc($pwaln);


Calculate pairwise statistics.


Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : number_of_comparable_bases
 Usage   : my $bases = $stat->number_of_comparable_bases($aln);
 Function: Returns the count of the number of bases that can be
           compared (L) in this alignment ( length - gaps)
 Returns : integer
 Args    : L<Bio::Align::AlignI>


 Title   : number_of_differences
 Usage   : my $nd = $stat->number_of_distances($aln);
 Function: Returns the number of differences between two sequences
 Returns : integer
 Args    : L<Bio::Align::AlignI>


 Title   : number_of_gaps
 Usage   : my $nd = $stat->number_of_gaps($aln);
 Function: Returns the number of gapped positions among sequences in alignment
 Returns : integer
 Args    : L<Bio::Align::AlignI>


 Title   : score_nuc
 Usage   : my $score = $stat->score_nuc($aln);
           my $score = $stat->score_nuc(
             -aln =>$aln,
             -match    => 1,
             -mismatch => -1,
             -gap_open => -1,
             -gap_ext  => -1
 Function: Calculate the score of an alignment of 2 nucleic acid sequences. The
           scoring parameters can be specified. Otherwise the blastn default
           parameters are used: match = 2, mismatch = -3, gap opening = -5, gap
           extension = -2
 Returns : alignment score (number)
 Args    : L<Bio::Align::AlignI>
           match score [optional]
           mismatch score [optional]
           gap opening score [optional]
           gap extension score [optional]