Name | Description | Type | Package | Framework |
AbstractMatrixAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
AbstractPairwiseSequenceAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
AbstractProfileProfileAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
AbstractScorer | Class | org.biojava.nbio.alignment.template | BioJava | |
Aligner | Defines an algorithm which computes an alignment Profile from a list of Sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
CallablePairwiseSequenceAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
CallablePairwiseSequenceScorer | Class | org.biojava.nbio.alignment.template | BioJava | |
CallableProfileProfileAligner | Class | org.biojava.nbio.alignment.template | BioJava | |
GapPenalty | Defines a data structure for the gap penalties used during a sequence alignment routine. | Interface | org.biojava.nbio.alignment.template | BioJava |
GapPenalty .Type | Defines the possible types of gap penalties. | Class | org.biojava.nbio.alignment.template | BioJava |
GuideTreeNode | Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment. | Interface | org.biojava.nbio.alignment.template | BioJava |
HierarchicalClusterer | Defines a clustering algorithm that converts a distance matrix into a tree. | Interface | org.biojava.nbio.alignment.template | BioJava |
MatrixAligner | Defines an Aligner which builds a score matrix during computation. | Interface | org.biojava.nbio.alignment.template | BioJava |
PairInProfileScorer | Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile. | Interface | org.biojava.nbio.alignment.template | BioJava |
PairwiseSequenceAligner | Defines an Aligner for a pair of Sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
PairwiseSequenceScorer | Defines an algorithm which computes a score for a pair of sequences. | Interface | org.biojava.nbio.alignment.template | BioJava |
PartitionRefiner | Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning. | Interface | org.biojava.nbio.alignment.template | BioJava |
ProfileProfileAligner | Defines an Aligner for a pair of Profiles. | Interface | org.biojava.nbio.alignment.template | BioJava |
ProfileProfileScorer | Defines an algorithm which computes a score for a pairing of alignment profiles. | Interface | org.biojava.nbio.alignment.template | BioJava |
RescoreRefiner | Interface | org.biojava.nbio.alignment.template | BioJava | |
Scorer | Defines an algorithm which computes a score. | Interface | org.biojava.nbio.alignment.template | BioJava |