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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 |
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