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>