- AbstractMatrixAligner
- AbstractPairwiseSequenceAligner
- AbstractProfileProfileAligner
- AbstractScorer
- Aligner
- AlignerHelper
- AlignerHelper.Anchor
- AlignerHelper.Anchor.QueryIndexComparator
- AlignerHelper.Cut
- AlignerHelper.Last
- AlignerHelper.Subproblem
- Alignments
- Alignments.PairInProfileScorerType
- Alignments.PairwiseSequenceAlignerType
- Alignments.PairwiseSequenceScorerType
- Alignments.ProfileProfileAlignerType
- Alignments.RefinerType
- AnchoredPairwiseSequenceAligner
- CallablePairwiseSequenceAligner
- CallablePairwiseSequenceScorer
- CallableProfileProfileAligner
- Comparison
- CookbookMSA
- DemoAlignProteins
- DemoDistanceTree
- DemoLoadSubstMax
- DistanceMatrixCalculator
- DistanceTreeEvaluator
- ForesterWrapper
- FractionalIdentityInProfileScorer
- FractionalIdentityScorer
- FractionalSimilarityInProfileScorer
- FractionalSimilarityScorer
- GapPenalty
- GapPenalty.Type
- GuanUberbacher
- GuideTree
- GuideTreeNode
- HierarchicalClusterer
- MatrixAligner
- NeedlemanWunsch
- PairInProfileScorer
- PairwiseSequenceAligner
- PairwiseSequenceScorer
- PartitionRefiner
- ProfileProfileAligner
- ProfileProfileScorer
- RescoreRefiner
- Scorer
- SimpleGapPenalty
- SimpleProfileProfileAligner
- SmithWaterman
- StandardRescoreRefiner
- StockholmFileAnnotation
- StockholmFileAnnotation.StockholmFileAnnotationReference
- StockholmFileParser
- StockholmStructure
- StockholmStructure.DatabaseReference
- SubstitutionMatrixScorer
- TestDNANeedlemanWunsch
- TreeConstructor
- TreeConstructorType
- TreeType