Uses of Interface
org.biojava.nbio.alignment.template.MatrixAligner

Packages that use MatrixAligner

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

Uses of MatrixAligner in org.biojava.nbio.alignment

Classes in org.biojava.nbio.alignment that implement MatrixAligner

Modifier and Type	Class and Description
class	NeedlemanWunsch<S extends Sequence<C>,C extends Compound> Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
class	SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> Implements a simple (naive) Aligner for a pair of Profiles.
class	SmithWaterman<S extends Sequence<C>,C extends Compound> Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).

Uses of MatrixAligner in org.biojava.nbio.alignment.routines

Classes in org.biojava.nbio.alignment.routines that implement MatrixAligner

Modifier and Type	Class and Description
class	AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
class	GuanUberbacher<S extends Sequence<C>,C extends Compound> Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).

Uses of MatrixAligner in org.biojava.nbio.alignment.template

Classes in org.biojava.nbio.alignment.template that implement MatrixAligner

Modifier and Type	Class and Description
class	AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> Implements common code for an Aligner which builds a score matrix during computation.
class	AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> Implements common code for an Aligner for a pair of Sequences.
class	AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> Implements common code for an Aligner for a pair of Profiles.