org.biojava3.alignment.template
Interfaces 
AlignedSequence
Aligner
GapPenalty
GuideTreeNode
HierarchicalClusterer
MatrixAligner
MutableAlignedSequence
MutableProfile
MutableProfilePair
MutableSequencePair
PairInProfileScorer
PairwiseSequenceAligner
PairwiseSequenceScorer
PartitionRefiner
Profile
ProfilePair
ProfileProfileAligner
ProfileProfileScorer
ProfileView
RescoreRefiner
Scorer
SequencePair
SubstitutionMatrix
Classes 
AbstractMatrixAligner
AbstractPairwiseSequenceAligner
AbstractProfileProfileAligner
AbstractScorer
CallablePairwiseSequenceAligner
CallablePairwiseSequenceScorer
CallableProfileProfileAligner
Enums 
AlignedSequence.Step
GapPenalty.Type
Profile.StringFormat