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See:
Description
Interface Summary | |
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MultipleAligner | |
PairwiseAligner | |
TracebackPlotter |
Class Summary | |
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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 | |
SequenceShuffler | Shuffles a sequence and aligns it again multiple times to give mean and variance of alignments on random sequences. |
SmithWaterman | |
SmithWatermanLinearSpace | |
SmithWatermanLinearSpaceAffine | |
Traceback |
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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