Package org.biojava.nbio.alignment
package org.biojava.nbio.alignment
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ClassDescriptionStatic utility to easily run alignment routines.List of implemented sequence pair in a profile scoring routines.List of implemented pairwise sequence alignment routines.List of implemented pairwise sequence scoring routines.List of implemented profile-profile alignment routines.List of implemented profile refinement routines.Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
Profile.Implements an algorithm which computes a score for a sequence alignment pair.Implements an algorithm which computes a score for a sequence alignment pair picked from an alignmentProfile.Implements an algorithm which computes a score for a sequence alignment pair.Implements a data structure for a guide tree used during progressive multiple sequence alignment.Implements a data structure for the gap penalties used during a sequence alignment routine.Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from eachSequence).Scores using a substitution matrix.