All Classes
AAindexFactory
AAIndexFileParser
AAIndexProvider
AbstractMatrixAligner
AbstractPairwiseSequenceAligner
AbstractProfileProfileAligner
AbstractScorer
AlignedSequence
AlignedSequence.Step
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
CookbookMSA
DefaultAAIndexProvider
DemoAlignProteins
DemoLoadSubstMax
FractionalIdentityInProfileScorer
FractionalIdentityScorer
FractionalSimilarityInProfileScorer
FractionalSimilarityScorer
GapPenalty
GapPenalty.Type
GuanUberbacher
GuideTree
GuideTreeNode
HierarchicalClusterer
MatrixAligner
MutableAlignedSequence
MutableProfile
MutableProfilePair
MutableSequencePair
NeedlemanWunsch
PairInProfileScorer
PairwiseSequenceAligner
PairwiseSequenceScorer
PartitionRefiner
Profile
Profile.StringFormat
ProfilePair
ProfileProfileAligner
ProfileProfileScorer
ProfileView
RescoreRefiner
ScaledSubstitutionMatrix
Scorer
SequencePair
SimpleAlignedSequence
SimpleGapPenalty
SimpleProfile
SimpleProfilePair
SimpleProfileProfileAligner
SimpleSequencePair
SimpleSubstitutionMatrix
SmithWaterman
StandardRescoreRefiner
StockholmFileAnnotation
StockholmFileAnnotation.StockholmFileAnnotationReference
StockholmFileParser
StockholmStructure
StockholmStructure.DatabaseReference
SubstitutionMatrix
SubstitutionMatrixHelper
SubstitutionMatrixScorer
TestDNANeedlemanWunsch