Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments
use strict; my $stats = Bio::Align::DNAStatistics->new(); # get alignment object of two sequences somehow my $pwaln; print $stats->number_of_comparable_bases($pwaln);
Calculate pairwise statistics.
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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>
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.