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All callbacks are optional. When there is just one way to make the
optimal alignment, the C<Algorithm::NeedlemanWunsch> object prefers
calling the specific callbacks, but will call C<select_align> if it's
defined and the specific callback isn't.

Note that C<select_align> is called I<instead> of the specific
callbacks, not in addition to them - users defining both
C<select_align> and other callbacks should probably call the specific
callback explicitly from their C<select_align>, once it decides which
one to prefer.

Also note that the passed positions move backwards, from the sequence
ends to zero - if you're building the alignment in your callbacks, add
items to the front.

=head2 Extensions

In addition to the standard Needleman-Wunsch algorithm, this module
also implements two popular extensions: local alignment and affine

lib/Algorithm/NeedlemanWunsch.pm  view on Meta::CPAN

Copyright 2007-2013 Vaclav Barta, all rights reserved.

This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.

=head1 CREDITS

The algorithm is defined by Saul Needleman and Christian Wunsch in "A
general method applicable to the search for similarities in the amino
acid sequence of two proteins", J Mol Biol. 48(3):443-53.

This implementation is based mostly on
L<http://www.ludwig.edu.au/course/lectures2005/Likic.pdf>, local
alignment is from
L<http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/node6.html>.

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