Uses of Class
org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner

Packages that use AbstractPairwiseSequenceAligner

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

Uses of AbstractPairwiseSequenceAligner in org.biojava.nbio.alignment

Subclasses of AbstractPairwiseSequenceAligner in org.biojava.nbio.alignment

Modifier and Type	Class	Description
class	NeedlemanWunsch<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
class	SmithWaterman<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).

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

Subclasses of AbstractPairwiseSequenceAligner in org.biojava.nbio.alignment.routines

Modifier and Type	Class	Description
class	AnchoredPairwiseSequenceAligner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>	Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).