## Uses of Package
org.biojava.bio.alignment

Packages that use org.biojava.bio.alignment
org.biojava.bio.alignment: Classes to generate and describe sequence alignments.
org.biojava.bio.structure.io: Input and Output of Structures

Classes in org.biojava.bio.alignment used by org.biojava.bio.alignment
AbstractULAlignment
AlignmentElement AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
ARAlignment ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
EditableAlignment EditableAlignment is an interface that defines methods for shifting bases within an Alignment.
IllegalAlignmentEditException The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.
NeedlemanWunsch Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence.
SequenceAlignment This Interface provides methods for the alignment of bio-sequences.
SubstitutionMatrix This object is able to read a substitution matrix file and constructs a short matrix in memory.
UnequalLengthAlignment UnequalLengthAlignment has the following behavior.

Classes in org.biojava.bio.alignment used by org.biojava.bio.structure.io
SubstitutionMatrix This object is able to read a substitution matrix file and constructs a short matrix in memory.