BioJava-1.7

Core biological packages

org.biojava.bibliography	The data structures and interfaces included in this package define an interoperable framework for bibliographic searches.
org.biojava.bio	The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.filter
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.biojava.bio.taxa	Taxonomy object for representing species information.
org.biojava.directory	Open Bio Sequence Database Access (OBDA) registry support.

User interface components

org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.gui.glyph	Glyphs implementations that draw shapes into SequenceRenderers
org.biojava.bio.gui.sequence	Graphical displays of biological sequences and associated annotations.
org.biojava.bio.gui.sequence.tracklayout	Classes for the handling of the layout of a WrappedSequencePanel.

Sequence databases and formats

org.biojava.bio.program.das	Development client for the Distributed Annotation System.
org.biojava.bio.program.das.dasalignment	request alignments via DAS
org.biojava.bio.program.homologene	Support classes for Homologene data.
org.biojava.bio.program.indexdb	A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.seq.db.biofetch	Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.emblcd	Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.
org.biojava.bio.seq.db.flat	Support for OBDA flatfile databases.
org.biojava.bio.seq.io.agave	Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.game	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.io.game12	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).

Handling output from external tools

org.biojava.bio.program	Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.blast2html	Code for generating HTML reports from blast output
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.sax	Parsers which offer XML representations of the output from common bioinformatics tools.
org.biojava.bio.program.sax.blastxml	Parsers for the XML output from NCBI blast.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.xml	Utility classes for the org.biojava.bio.program.sax package.

Dynamic programming packages

org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.dp.onehead
org.biojava.bio.dp.twohead

Chromatogram and trace file support

org.biojava.bio.chromatogram	Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.chromatogram.graphic	Tools for displaying chromatograms.
org.biojava.bio.program.abi	ABI Trace Handling.
org.biojava.bio.program.scf	Support for the SCF chromatogram format.

Macromolecular structure (PDB)

org.biojava.bio.program.das.dasstructure	request a protein structure via DAS
org.biojava.bio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align	Classes for the super-imposition of structures.
org.biojava.bio.structure.align.helper	Helper classes for structural alignment.
org.biojava.bio.structure.align.pairwise	Classes for the pairwise alignment of structures.
org.biojava.bio.structure.gui	A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.bio.structure.io	Input and Output of Structures
org.biojava.bio.structure.jama	Matrix package for from JAMA
org.biojava.bio.structure.server	classes for easier management of PDB installations

Utilities and developers' packages

org.biojava.bio.program.tagvalue	Process files as streams of records, each with tags with values.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io.filterxml	Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojava.naming
org.biojava.ontology	A general-purpose API for ontologies.
org.biojava.ontology.io	Tools for loading and saving ontologies.
org.biojava.utils	Miscellaneous utility classes used by other BioJava components.
org.biojava.utils.automata
org.biojava.utils.cache	A simple cache system with pluggable caching behaviours.
org.biojava.utils.candy	The data structures and interfaces included in this package define an interoperable framework for simple controlled vocabularies.
org.biojava.utils.io	I/O utility classes.
org.biojava.utils.math	Mathematical utility classes.
org.biojava.utils.net	Network programming utility classes.
org.biojava.utils.process	Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.
org.biojava.utils.regex	This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets.
org.biojava.utils.stax	The Stack API for XML (StAX).
org.biojava.utils.walker
org.biojava.utils.xml	Utility classes for handling and generating XML documents.

Molecular biology packages

org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.proteomics	Utilities to aid in performing various physical analysis of proteins.
org.biojava.bio.proteomics.aaindex	Classes and interfaces to load Amino Acid Index database files.

Experimental packages

org.biojava.bio.annodb	Databases of generic structured data (annotation) objects.
org.biojava.bio.program.formats	Experimental parsers using the tagvalue framework.
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.seq.distributed	Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.stats.svm	Support Vector Machine classification and regression.
org.biojava.stats.svm.tools	Tools for use of the SVM package.
org.biojava.utils.lsid	Life Science Identifier (LSID) package.

Biojava extension (biojavax) packages

org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality
org.biojavax.bio	Classes to represent biological entities and their relationships.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.
org.biojavax.bio.taxa	Objects that model the NCBI taxonomy schema as described in the BioSQL schema.
org.biojavax.bio.taxa.io
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.
org.biojavax.utils	Utility classes that are used by biojavax objects but could have wider utility to other applications.

Genetic Algorithm Framework

org.biojavax.ga	Classes to provide a genetic algorithm framework
org.biojavax.ga.exception	Exceptions related to the GA framework
org.biojavax.ga.functions	GA functions
org.biojavax.ga.impl	Default implementations and abstract classes.
org.biojavax.ga.util	Utility functions and helper classes

Experimental Phylogeny packages

org.biojavax.bio.phylo	Classes to support phlylogeny objects.
org.biojavax.bio.phylo.io.nexus	Classes to support the I/O of Nexus files.
org.biojavax.bio.phylo.io.phylip	Classes to support the reading and writing of PHYLIP format.

Other Packages

org.biojava.bio.structure.gui.events	Some event classes for the protein structure GUIs.
org.biojava.bio.structure.gui.util	Some utility classes for the protein structure GUIs.
org.biojava.bio.structure.io.mmcif	Input and Output of mmcif files
org.biojava.bio.structure.io.mmcif.chem
org.biojava.bio.structure.io.mmcif.model	Datamodel objects used for processing mmcif files.
org.biojava.ontology.obo