Package no.uio.labmed.biojava.alignment

Interface Summary
AlignerInterface Interface defining a sequence aligner: one that is used to produce sequence alignments.
ScoreInterface Interface defining alignment scoring.

Class Summary
AbstractAligner Abstract implementation of the AlignerInterface.
ScoreIdentity Implementation of ScoreInterface which scores identity.
ScoreMatrix Alignment scoring matrix, eg.
SimpleAligner Implementation of the Needleman-Wunsch and Smith-Waterman algorithm for sequence alignment.
StringSequenceTools Helper class for making sequences over the alphabet of characters.
Test Test program.