NAME

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

SYNOPSIS

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

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

DESCRIPTION

Calculate pairwise statistics.

FEEDBACK

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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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:

  http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

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

number_of_comparable_bases

 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>

number_of_differences

 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>

number_of_gaps

 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>

CPAN RT