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 BasicScoringScheme
 CharSequence
 CrochemoreLandauZivUkelson
 CrochemoreLandauZivUkelsonGlobalAlignment
 CrochemoreLandauZivUkelsonLocalAlignment
 Factor
 FactorSequence
 IncompatibleScoringSchemeException
 InvalidScoringMatrixException
 InvalidSequenceException
 LocalAlignmentBlock
 Matrix
 NeedlemanWunsch
 NeoBio
 NeoBio
 OutMatrix
 PairwiseAlignment
 PairwiseAlignmentAlgorithm
 PairwiseAlignmentFrame
 RandomFactorSequenceGenerator
 RandomSequenceGenerator
 ScoringMatrix
 ScoringScheme
 Smawk
 SmithWaterman
 Trie
 
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