Package jebl.evolution.align

Provides classes and interfaces for pairwise alignment of two sequences.

See: Description

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

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