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# 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 |

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