org.jscience.biology.alignment
Interfaces 
Matrix
Classes 
AlignmentBlock
BasicScoringScheme
CharSequence
CrochemoreLandauZivUkelson
CrochemoreLandauZivUkelsonGlobalAlignment
CrochemoreLandauZivUkelsonLocalAlignment
Factor
FactorSequence
LocalAlignmentBlock
NeedlemanWunsch
OutMatrix
PairwiseAlignment
PairwiseAlignmentAlgorithm
ScoringMatrix
ScoringScheme
Smawk
SmithWaterman
Trie
Exceptions 
IncompatibleScoringSchemeException
InvalidScoringMatrixException
InvalidSequenceException