Uses of Package
org.biojava.bio.alignment

Packages that use org.biojava.bio.alignment

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.chromatogram	Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.program.abi	ABI Trace Handling.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojavax.bio.phylo.io.phylip	Classes to support the reading and writing of PHYLIP format.

Classes in org.biojava.bio.alignment used by org.biojava.bio.alignment

Class	Description
AbstractULAlignment
Alignment	An alignment containing multiple SymbolLists.
AlignmentAlgorithm	This Interface provides methods for the alignment of bio-sequences.
AlignmentElement	AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
AlignmentPair	This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
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.
SimpleAlignment	A simple implementation of an Alignment.
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.chromatogram

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.dist

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.dp

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.program.abi

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.program.phred

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.search

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.seq.homol

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.seq.impl

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.seq.io

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojava.bio.symbol

Class	Description
Alignment	An alignment containing multiple SymbolLists.

Classes in org.biojava.bio.alignment used by org.biojavax.bio.phylo.io.phylip

Class	Description
Alignment	An alignment containing multiple SymbolLists.