org.biojava3.alignment
Classes 
Alignments
FractionalIdentityInProfileScorer
FractionalIdentityScorer
FractionalSimilarityInProfileScorer
FractionalSimilarityScorer
GuideTree
NeedlemanWunsch
SimpleAlignedSequence
SimpleGapPenalty
SimpleProfile
SimpleProfilePair
SimpleProfileProfileAligner
SimpleSequencePair
SimpleSubstitutionMatrix
SmithWaterman
StandardRescoreRefiner
SubstitutionMatrixHelper
Enums 
Alignments.PairInProfileScorerType
Alignments.PairwiseSequenceAlignerType
Alignments.PairwiseSequenceScorerType
Alignments.ProfileProfileAlignerType
Alignments.RefinerType