# Hierarchy For Package jebl.evolution.align

Package Hierarchies:

- All Packages

## Class Hierarchy

- java.lang.Object
  - jebl.evolution.align.Align
    - jebl.evolution.align.MaximalSegmentPair
    - jebl.evolution.align.NeedlemanWunsch
    - jebl.evolution.align.NeedlemanWunschAffine
    - jebl.evolution.align.NeedlemanWunschLinearSpace
    - jebl.evolution.align.NeedlemanWunschLinearSpaceAffine (implements jebl.evolution.align.PairwiseAligner)
    - jebl.evolution.align.NonOverlapMultipleLocalAffine
    - jebl.evolution.align.OldNeedlemanWunschAffine
    - jebl.evolution.align.OverlapAlign
    - jebl.evolution.align.SmithWaterman
    - jebl.evolution.align.SmithWatermanLinearSpace
    - jebl.evolution.align.SmithWatermanLinearSpaceAffine
  - jebl.evolution.align.AlignCommand
  - jebl.evolution.align.AlignmentTreeBuilderFactory
  - jebl.evolution.align.AlignmentTreeBuilderFactory.Result
  - jebl.evolution.align.BartonSternberg (implements jebl.evolution.align.MultipleAligner)
  - jebl.evolution.distances.BasicDistanceMatrix (implements jebl.evolution.distances.DistanceMatrix)
    - jebl.evolution.align.SequenceAlignmentsDistanceMatrix
  - jebl.evolution.align.Output
    - jebl.evolution.align.SystemOut
  - jebl.evolution.align.PairwiseAligner.Result
  - jebl.evolution.align.ProfileCharacter
  - jebl.evolution.align.SequenceShuffler
  - jebl.evolution.align.Traceback

## Interface Hierarchy

- jebl.evolution.align.MultipleAligner
- jebl.evolution.align.PairwiseAligner
- jebl.evolution.align.TracebackPlotter