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