Packages 
Package Description
demo  
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.embl  
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.reference  
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.io.fastq
FASTQ and variants sequence format I/O.
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
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.structure
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.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.quaternary  
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.basepairs  
org.biojava.nbio.structure.cath  
org.biojava.nbio.structure.chem  
org.biojava.nbio.structure.cluster  
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.geometry  
org.biojava.nbio.structure.gui
org.biojava.nbio.structure.gui.events
org.biojava.nbio.structure.gui.util
org.biojava.nbio.structure.gui.util.color  
org.biojava.nbio.structure.io
Input and Output of Structures
org.biojava.nbio.structure.io.cif  
org.biojava.nbio.structure.io.mmtf  
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.scop
org.biojava.nbio.structure.secstruc  
org.biojava.nbio.structure.symmetry.axis  
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.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