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#Org.biojava.nbio.alignment.template Classes and Interfaces - 21 results found.
NameDescriptionTypePackageFramework
AbstractMatrixAlignerClassorg.biojava.nbio.alignment.templateBioJava
AbstractPairwiseSequenceAlignerClassorg.biojava.nbio.alignment.templateBioJava
AbstractProfileProfileAlignerClassorg.biojava.nbio.alignment.templateBioJava
AbstractScorerClassorg.biojava.nbio.alignment.templateBioJava
AlignerDefines an algorithm which computes an alignment Profile from a list of Sequences.Interfaceorg.biojava.nbio.alignment.templateBioJava
CallablePairwiseSequenceAlignerClassorg.biojava.nbio.alignment.templateBioJava
CallablePairwiseSequenceScorerClassorg.biojava.nbio.alignment.templateBioJava
CallableProfileProfileAlignerClassorg.biojava.nbio.alignment.templateBioJava
GapPenaltyDefines a data structure for the gap penalties used during a sequence alignment routine.Interfaceorg.biojava.nbio.alignment.templateBioJava
GapPenalty .TypeDefines the possible types of gap penalties.Classorg.biojava.nbio.alignment.templateBioJava
GuideTreeNodeDefines a data structure for the node in a guide tree used during progressive multiple sequence alignment.Interfaceorg.biojava.nbio.alignment.templateBioJava
HierarchicalClustererDefines a clustering algorithm that converts a distance matrix into a tree.Interfaceorg.biojava.nbio.alignment.templateBioJava
MatrixAlignerDefines an Aligner which builds a score matrix during computation.Interfaceorg.biojava.nbio.alignment.templateBioJava
PairInProfileScorerDefines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.Interfaceorg.biojava.nbio.alignment.templateBioJava
PairwiseSequenceAlignerDefines an Aligner for a pair of Sequences.Interfaceorg.biojava.nbio.alignment.templateBioJava
PairwiseSequenceScorerDefines an algorithm which computes a score for a pair of sequences.Interfaceorg.biojava.nbio.alignment.templateBioJava
PartitionRefinerDefines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.Interfaceorg.biojava.nbio.alignment.templateBioJava
ProfileProfileAlignerDefines an Aligner for a pair of Profiles.Interfaceorg.biojava.nbio.alignment.templateBioJava
ProfileProfileScorerDefines an algorithm which computes a score for a pairing of alignment profiles.Interfaceorg.biojava.nbio.alignment.templateBioJava
RescoreRefinerInterfaceorg.biojava.nbio.alignment.templateBioJava
ScorerDefines an algorithm which computes a score.Interfaceorg.biojava.nbio.alignment.templateBioJava