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.\" ========================================================================
.\"
.IX Title "Bio::Align::PairwiseStatistics 3pm"
.TH Bio::Align::PairwiseStatistics 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Align::PairwiseStatistics \- Base statistic object for Pairwise Alignments
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  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);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Calculate pairwise statistics.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "number_of_comparable_bases"
.IX Subsection "number_of_comparable_bases"
.Vb 6
\& 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>
.Ve
.SS "number_of_differences"
.IX Subsection "number_of_differences"
.Vb 5
\& 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>
.Ve
.SS "number_of_gaps"
.IX Subsection "number_of_gaps"
.Vb 5
\& 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>
.Ve
.SS "score_nuc"
.IX Subsection "score_nuc"
.Vb 10
\& Title   : score_nuc
\& Usage   : my $score = $stat\->score_nuc($aln);
\&             or
\&           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]
.Ve