# Package jebl.evolution.align

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

Related Packages
Package
Description
jebl.evolution.align.scores
Class
Description
Align
AlignCommand
A command line interface for the algorithms in jebl.evolution.align.
AlignmentTreeBuilderFactory
AlignmentTreeBuilderFactory.Result
BartonSternberg
MaximalSegmentPair
MultipleAligner
NeedlemanWunsch
NeedlemanWunschAffine
NeedlemanWunschLinearSpace
NeedlemanWunschLinearSpaceAffine
NonOverlapMultipleLocalAffine
Performs recursive local alignments.
OldNeedlemanWunschAffine
Output
OverlapAlign
PairwiseAligner
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
TracebackPlotter