Core Packages
org.biojava.bio: The core classes that will be used throughout the bio packages.
org.biojava.bio.dist: Probability distributions over Alphabets.
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.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.

CORBA Packages
GNOME
org.Biocorba.Seqcore
org.biojava.bridge.Biocorba.Seqcore
org.biojava.bridge.GNOME

External Tools
org.biojava.bio.program: Java wrappers for interacting with external bioinformatics tools.
org.biojava.bio.program.gff: GFF manipulation.

Development Packages
org.biojava.bio.dp: HMM and Dynamic Programming Algorithms.
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.xml: This package contains a number of utilities for processing XML documents.

ACeDB Connection Packages
org.acedb: Bindings to ACeDB.
org.acedb.seq: The bridge from AceDB objects to biojava implementations.
org.acedb.socket: An implementation of an ACeDB database for use with the ACeDB socket server.
org.acedb.staticobj: Implementations of the ACeDB data nodes which are vanilla java.

Other Packages
org.biojava.bio.gui: Graphical interfaces for biojava objects.
org.biojava.bio.gui.sequence: Graphical displays of biological sequences and associated annotations (highly experimental).
org.biojava.bio.search
org.biojava.utils: Miscellaneous utility classes used by other BioJava components.
org.biojava.utils.contract