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