Package jebl.evolution.align
Provides classes and interfaces for pairwise alignment of two sequences.
All major algorithms including Smith-Waterman and Needleman-Wunsch
are implemented.
Some of the classes in this package are based on source code by Peter Sestoft, sestoft@dina.kvl.dk. His original source code can be at http://www.dina.kvl.dk/~sestoft/bsa.html
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Interface Summary Interface Description MultipleAligner PairwiseAligner TracebackPlotter -
Class Summary Class Description Align AlignCommand A command line interface for the algorithms in jebl.evolution.align.AlignmentTreeBuilderFactory AlignmentTreeBuilderFactory.Result BartonSternberg MaximalSegmentPair NeedlemanWunsch NeedlemanWunschAffine NeedlemanWunschLinearSpace NeedlemanWunschLinearSpaceAffine NonOverlapMultipleLocalAffine Performs recursive local alignments.OldNeedlemanWunschAffine Output OverlapAlign PairwiseAligner.Result ProfileCharacter SequenceAlignmentsDistanceMatrix Builds a distance matrix by performing a series of pairwise alignments between the specified sequences (unlike the methods in jebl.evolution.distances, which extract the pairwise distances from a multiple sequence alignment).SequenceShuffler Shuffles a sequence and aligns it again multiple times to give mean and variance of alignments on random sequences.SmithWaterman SmithWatermanLinearSpace SmithWatermanLinearSpaceAffine SystemOut Traceback