Package jebl.evolution.align

Provides classes and interfaces for pairwise alignment of two sequences.

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  
 

Package jebl.evolution.align Description

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