Packages 
Package Description
org.biojava.nbio.aaproperties
Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.
org.biojava.nbio.aaproperties.profeat
Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.
org.biojava.nbio.aaproperties.profeat.convertor
Set of classes that enable the conversion protein sequences into various attributes.
org.biojava.nbio.aaproperties.xml
Set of classes that handles the reading and writing of xml files.
org.biojava.nbio.alignment  
org.biojava.nbio.alignment.io  
org.biojava.nbio.alignment.routines  
org.biojava.nbio.alignment.template  
org.biojava.nbio.core.alignment  
org.biojava.nbio.core.alignment.matrices  
org.biojava.nbio.core.alignment.template  
org.biojava.nbio.core.exceptions  
org.biojava.nbio.core.search.io  
org.biojava.nbio.core.search.io.blast  
org.biojava.nbio.core.sequence  
org.biojava.nbio.core.sequence.compound  
org.biojava.nbio.core.sequence.edits  
org.biojava.nbio.core.sequence.features  
org.biojava.nbio.core.sequence.io  
org.biojava.nbio.core.sequence.io.template  
org.biojava.nbio.core.sequence.io.util  
org.biojava.nbio.core.sequence.loader  
org.biojava.nbio.core.sequence.location  
org.biojava.nbio.core.sequence.location.template  
org.biojava.nbio.core.sequence.storage  
org.biojava.nbio.core.sequence.template  
org.biojava.nbio.core.sequence.transcription  
org.biojava.nbio.core.sequence.views  
org.biojava.nbio.core.util  
org.biojava.nbio.data.sequence
Set of classes that responsible for data handling.
org.biojava.nbio.genome  
org.biojava.nbio.genome.homology  
org.biojava.nbio.genome.parsers.cytoband  
org.biojava.nbio.genome.parsers.geneid  
org.biojava.nbio.genome.parsers.genename  
org.biojava.nbio.genome.parsers.gff  
org.biojava.nbio.genome.parsers.twobit  
org.biojava.nbio.genome.query  
org.biojava.nbio.genome.uniprot  
org.biojava.nbio.genome.util  
org.biojava.nbio.ontology  
org.biojava.nbio.ontology.io
Tools for loading and saving ontologies.
org.biojava.nbio.ontology.obo  
org.biojava.nbio.ontology.utils  
org.biojava.nbio.phosphosite  
org.biojava.nbio.phylo  
org.biojava.nbio.proteincomparisontool  
org.biojava.nbio.protmod  
org.biojava.nbio.protmod.io  
org.biojava.nbio.protmod.structure  
org.biojava.nbio.ronn
BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence.
org.biojava.nbio.sequencing.io.fastq
FASTQ and variants sequence format I/O.
org.biojava.nbio.structure
Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align
Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce
Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.client
This package deals with the server communication for auto-downloading pre-calculated alignments.
org.biojava.nbio.structure.align.events  
org.biojava.nbio.structure.align.fatcat
Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.
org.biojava.nbio.structure.align.fatcat.calc  
org.biojava.nbio.structure.align.gui  
org.biojava.nbio.structure.align.gui.aligpanel  
org.biojava.nbio.structure.align.gui.autosuggest  
org.biojava.nbio.structure.align.gui.jmol
Utility methods for better interaction with Jmol.
org.biojava.nbio.structure.align.helper
Helper classes for structural alignment.
org.biojava.nbio.structure.align.model  
org.biojava.nbio.structure.align.multiple  
org.biojava.nbio.structure.align.multiple.mc  
org.biojava.nbio.structure.align.multiple.util  
org.biojava.nbio.structure.align.pairwise
Classes for the pairwise alignment of structures.
org.biojava.nbio.structure.align.seq  
org.biojava.nbio.structure.align.util  
org.biojava.nbio.structure.align.webstart
Classes related to Java Web Start
org.biojava.nbio.structure.align.xml
Serialization and deserialization for structure alignment results (as AFPChain object) to XML.
org.biojava.nbio.structure.asa  
org.biojava.nbio.structure.cath  
org.biojava.nbio.structure.contact  
org.biojava.nbio.structure.domain  
org.biojava.nbio.structure.domain.pdp  
org.biojava.nbio.structure.ecod  
org.biojava.nbio.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.nbio.structure.gui.events
Some event classes for the protein structure GUIs.
org.biojava.nbio.structure.gui.util
Some utility classes for the protein structure GUIs.
org.biojava.nbio.structure.gui.util.color  
org.biojava.nbio.structure.io
Input and Output of Structures
org.biojava.nbio.structure.io.mmcif
Input and Output of mmcif files.
org.biojava.nbio.structure.io.mmcif.chem  
org.biojava.nbio.structure.io.mmcif.model
Datamodel objects used for processing mmcif files.
org.biojava.nbio.structure.io.sifts  
org.biojava.nbio.structure.io.util  
org.biojava.nbio.structure.jama
Matrix package for from JAMA
org.biojava.nbio.structure.math  
org.biojava.nbio.structure.quaternary  
org.biojava.nbio.structure.quaternary.io  
org.biojava.nbio.structure.rcsb  
org.biojava.nbio.structure.scop
org.biojava.nbio.structure.scop.server  
org.biojava.nbio.structure.secstruc  
org.biojava.nbio.structure.symmetry.analysis  
org.biojava.nbio.structure.symmetry.core  
org.biojava.nbio.structure.symmetry.geometry  
org.biojava.nbio.structure.symmetry.gui  
org.biojava.nbio.structure.symmetry.internal  
org.biojava.nbio.structure.symmetry.jmolScript  
org.biojava.nbio.structure.symmetry.misc  
org.biojava.nbio.structure.symmetry.utils  
org.biojava.nbio.structure.validation  
org.biojava.nbio.structure.xtal  
org.biojava.nbio.structure.xtal.io  
org.biojava.nbio.survival.cox  
org.biojava.nbio.survival.cox.comparators  
org.biojava.nbio.survival.cox.matrix  
org.biojava.nbio.survival.cox.stats  
org.biojava.nbio.survival.data  
org.biojava.nbio.survival.kaplanmeier.figure  
org.biojava.nbio.survival.kaplanmeier.metadata  
org.biojava.nbio.ws.alignment
This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava.nbio.ws.alignment.qblast  
org.biojava.nbio.ws.hmmer  
org.forester.analysis  
org.forester.application  
org.forester.applications  
org.forester.archaeopteryx  
org.forester.archaeopteryx.phylogeny.data  
org.forester.archaeopteryx.tools  
org.forester.archaeopteryx.webservices  
org.forester.datastructures  
org.forester.development  
org.forester.evoinference  
org.forester.evoinference.distance  
org.forester.evoinference.matrix.character  
org.forester.evoinference.matrix.distance  
org.forester.evoinference.parsimony  
org.forester.evoinference.tools  
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.data  
org.forester.io.parsers.tol  
org.forester.io.parsers.util  
org.forester.io.writers  
org.forester.msa  
org.forester.msa_compactor  
org.forester.pccx  
org.forester.phylogeny  
org.forester.phylogeny.data  
org.forester.phylogeny.factories  
org.forester.phylogeny.iterators  
org.forester.protein  
org.forester.rio  
org.forester.sdi  
org.forester.sequence  
org.forester.species  
org.forester.surfacing  
org.forester.test  
org.forester.test.examples  
org.forester.tools  
org.forester.util  
org.forester.ws.hmmer  
org.forester.ws.seqdb  
org.forester.ws.wabi  
org.jcolorbrewer  
org.jcolorbrewer.ui