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See:
Description
| Interface Summary | |
|---|---|
| MultipleAligner | |
| PairwiseAligner | |
| TracebackPlotter | |
| Class Summary | |
|---|---|
| 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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