org.biojava.bio.alignment

Interfaces

• Alignment
• AlignmentElement
• ARAlignment
• EditableAlignment
• QualitativeAlignment
• UnequalLengthAlignment

Classes

• AbstractULAlignment
• Alignment.SymbolListIterator
• AlignmentAlgorithm
• AlignmentPair
• FlexibleAlignment
• NeedlemanWunsch
• SimpleAlignment
• SimpleAlignmentElement
• SmithWaterman
• SubstitutionMatrix

Exceptions

• IllegalAlignmentEditException