Packages
org.biojava.bio.structure Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align Classes for the alignment of structures.
org.biojava.bio.structure.align.ce Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.bio.structure.align.client This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.bio.structure.align.events  
org.biojava.bio.structure.align.fatcat Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.bio.structure.align.fatcat.calc  
org.biojava.bio.structure.align.gui  
org.biojava.bio.structure.align.gui.aligpanel  
org.biojava.bio.structure.align.gui.autosuggest  
org.biojava.bio.structure.align.gui.jmol Utility methods for better interaction with Jmol.
org.biojava.bio.structure.align.helper Helper classes for structural alignment.
org.biojava.bio.structure.align.model  
org.biojava.bio.structure.align.pairwise Classes for the pairwise alignment of structures.
org.biojava.bio.structure.align.seq  
org.biojava.bio.structure.align.util  
org.biojava.bio.structure.align.webstart Classes related to Java Web Start
org.biojava.bio.structure.align.xml Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.bio.structure.domain  
org.biojava.bio.structure.domain.pdp  
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.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.gui.util.color  
org.biojava.bio.structure.io Input and Output of Structures
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.bio.structure.io.sifts  
org.biojava.bio.structure.io.util  
org.biojava.bio.structure.jama Matrix package for from JAMA
org.biojava.bio.structure.scop Parsers and API for SCOP, Structural Classification of Proteins.
org.biojava.bio.structure.scop.server  
org.biojava.bio.structure.secstruc  
org.biojava.bio.structure.server classes for easier management of PDB installations As of BioJava 3.0.2 this package is deprecated.
org.biojava3.aaproperties Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava3.aaproperties.profeat Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava3.aaproperties.profeat.convertor Set of classes that enable the conversion protein sequences into various attributes.
org.biojava3.aaproperties.xml Set of classes that handles the reading and writing of xml files.
org.biojava3.alignment  
org.biojava3.alignment.aaindex  
org.biojava3.alignment.routines  
org.biojava3.alignment.template  
org.biojava3.core.exceptions  
org.biojava3.core.sequence  
org.biojava3.core.sequence.compound  
org.biojava3.core.sequence.edits  
org.biojava3.core.sequence.features  
org.biojava3.core.sequence.io  
org.biojava3.core.sequence.io.template  
org.biojava3.core.sequence.io.util  
org.biojava3.core.sequence.loader  
org.biojava3.core.sequence.location  
org.biojava3.core.sequence.location.template  
org.biojava3.core.sequence.storage  
org.biojava3.core.sequence.template  
org.biojava3.core.sequence.transcription  
org.biojava3.core.sequence.views  
org.biojava3.core.util  
org.biojava3.data.sequence Set of classes that responsible for data handling.
org.biojava3.genome  
org.biojava3.genome.homology  
org.biojava3.genome.parsers.geneid  
org.biojava3.genome.parsers.gff  
org.biojava3.genome.query  
org.biojava3.genome.uniprot  
org.biojava3.genome.util  
org.biojava3.phylo  
org.biojava3.protmod  
org.biojava3.protmod.io  
org.biojava3.protmod.structure  
org.biojava3.ronn BioJava provide a module biojava3-protein-disorder for prediction disordered regions from a protein sequence.
org.biojava3.sequencing.io.fastq FASTQ and variants sequence format I/O.
org.biojava3.structure.gui New MVC interface for structure-gui
org.biojava3.ws.alignment This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava3.ws.alignment.qblast  
org.biojava3.ws.hmmer  
org.forester.application  
org.forester.archaeopteryx  
org.forester.archaeopteryx.phylogeny.data  
org.forester.archaeopteryx.webservices  
org.forester.datastructures  
org.forester.development  
org.forester.go  
org.forester.go.etc  
org.forester.io.parsers  
org.forester.io.parsers.nexus  
org.forester.io.parsers.nhx  
org.forester.io.parsers.phyloxml  
org.forester.io.parsers.phyloxml.phylogenydata  
org.forester.io.parsers.tol  
org.forester.io.writers  
org.forester.pccx  
org.forester.phylogeny  
org.forester.phylogeny.data  
org.forester.phylogeny.factories  
org.forester.phylogeny.iterators  
org.forester.phylogenyinference  
org.forester.sdi  
org.forester.surfacing  
org.forester.test  
org.forester.tools  
org.forester.util