All Classes
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