Uses of Package
org.biojava.nbio.alignment

Packages that use org.biojava.nbio.alignment

Package	Description
org.biojava.nbio.alignment
org.biojava.nbio.alignment.template

Classes in org.biojava.nbio.alignment used by org.biojava.nbio.alignment

Class and Description
Alignments.PairInProfileScorerType List of implemented sequence pair in a profile scoring routines.
Alignments.PairwiseSequenceAlignerType List of implemented pairwise sequence alignment routines.
Alignments.PairwiseSequenceScorerType List of implemented pairwise sequence scoring routines.
Alignments.ProfileProfileAlignerType List of implemented profile-profile alignment routines.
Alignments.RefinerType List of implemented profile refinement routines.
FractionalIdentityScorer Implements an algorithm which computes a score for a sequence alignment pair.
FractionalSimilarityScorer Implements an algorithm which computes a score for a sequence alignment pair.
GuideTree Implements a data structure for a guide tree used during progressive multiple sequence alignment.
GuideTree.Node Implements a data structure for the node in a guide tree used during progressive multiple sequence alignment.

Classes in org.biojava.nbio.alignment used by org.biojava.nbio.alignment.template

Class and Description
Alignments.PairInProfileScorerType List of implemented sequence pair in a profile scoring routines.
Alignments.ProfileProfileAlignerType List of implemented profile-profile alignment routines.