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<div class="header">
<h1 class="title">BioJava-1.7.1</h1>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Core biological packages table, listing packages, and an explanation">
<caption><span>Core biological packages</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bibliography/package-summary.html">org.biojava.bibliography</a></td>
<td class="colLast">
<div class="block">The data structures and interfaces included in this package define an
interoperable framework for bibliographic searches.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/package-summary.html">org.biojava.bio</a></td>
<td class="colLast">
<div class="block">The core classes that will be used throughout the bio packages.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/alignment/package-summary.html">org.biojava.bio.alignment</a></td>
<td class="colLast">
<div class="block">
Classes to generate and describe sequence alignments.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/dist/package-summary.html">org.biojava.bio.dist</a></td>
<td class="colLast">
<div class="block">
Probability distributions over Alphabets.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/search/package-summary.html">org.biojava.bio.search</a></td>
<td class="colLast">
<div class="block">
Interfaces and classes for representing sequence similarity search results.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/package-summary.html">org.biojava.bio.seq</a></td>
<td class="colLast">
<div class="block">Classes and interfaces for defining biological sequences and informatics
objects.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/seq/db/package-summary.html">org.biojava.bio.seq.db</a></td>
<td class="colLast">
<div class="block">
Collections of biological sequence data.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/filter/package-summary.html">org.biojava.bio.seq.filter</a></td>
<td class="colLast">&nbsp;</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/seq/io/package-summary.html">org.biojava.bio.seq.io</a></td>
<td class="colLast">
<div class="block">Classes and interfaces for processing and producing flat-file representations
of sequences.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/symbol/package-summary.html">org.biojava.bio.symbol</a></td>
<td class="colLast">
<div class="block">Representation of the Symbols that make up a sequence, and locations within
them.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/taxa/package-summary.html">org.biojava.bio.taxa</a></td>
<td class="colLast">
<div class="block">Taxonomy object for representing species information.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/directory/package-summary.html">org.biojava.directory</a></td>
<td class="colLast">
<div class="block">Open Bio Sequence Database Access (OBDA) registry support.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="User interface components table, listing packages, and an explanation">
<caption><span>User interface components</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/gui/package-summary.html">org.biojava.bio.gui</a></td>
<td class="colLast">
<div class="block">Graphical interfaces for biojava objects.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/gui/glyph/package-summary.html">org.biojava.bio.gui.glyph</a></td>
<td class="colLast">
<div class="block">Glyphs implementations that draw shapes into SequenceRenderers</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/gui/sequence/package-summary.html">org.biojava.bio.gui.sequence</a></td>
<td class="colLast">
<div class="block">
Graphical displays of biological sequences and associated annotations.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/gui/sequence/tracklayout/package-summary.html">org.biojava.bio.gui.sequence.tracklayout</a></td>
<td class="colLast">
<div class="block">Classes for the handling of the layout of a WrappedSequencePanel.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Sequence databases and formats table, listing packages, and an explanation">
<caption><span>Sequence databases and formats</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/das/package-summary.html">org.biojava.bio.program.das</a></td>
<td class="colLast">
<div class="block">Development client for the Distributed Annotation System.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/das/dasalignment/package-summary.html">org.biojava.bio.program.das.dasalignment</a></td>
<td class="colLast">
<div class="block">
request alignments via DAS</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/homologene/package-summary.html">org.biojava.bio.program.homologene</a></td>
<td class="colLast">
<div class="block">
Support classes for Homologene data.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/indexdb/package-summary.html">org.biojava.bio.program.indexdb</a></td>
<td class="colLast">
<div class="block">A flat-file ascii index of ascii flat files as per the OBDA specification.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/xff/package-summary.html">org.biojava.bio.program.xff</a></td>
<td class="colLast">
<div class="block">Event-driven parsing system for the Extensible Feature Format (XFF).</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/db/biofetch/package-summary.html">org.biojava.bio.seq.db.biofetch</a></td>
<td class="colLast">
<div class="block">Client for the OBDA BioFetch protocol.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/seq/db/biosql/package-summary.html">org.biojava.bio.seq.db.biosql</a></td>
<td class="colLast">
<div class="block">General purpose Sequence storage in a relational database.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/db/emblcd/package-summary.html">org.biojava.bio.seq.db.emblcd</a></td>
<td class="colLast">
<div class="block">
Readers for the EMBL CD-ROM format binary index files used by EMBOSS and Staden packages.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/seq/db/flat/package-summary.html">org.biojava.bio.seq.db.flat</a></td>
<td class="colLast">
<div class="block">
Support for OBDA flatfile databases.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/io/agave/package-summary.html">org.biojava.bio.seq.io.agave</a></td>
<td class="colLast">
<div class="block">Classes for converting between AGAVE XML and BioJava objects.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/seq/io/game/package-summary.html">org.biojava.bio.seq.io.game</a></td>
<td class="colLast">
<div class="block">Event-driven parsing system for the Gene Annotation Markup Elements (GAME).</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/io/game12/package-summary.html">org.biojava.bio.seq.io.game12</a></td>
<td class="colLast">
<div class="block">
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Handling output from external tools table, listing packages, and an explanation">
<caption><span>Handling output from external tools</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/package-summary.html">org.biojava.bio.program</a></td>
<td class="colLast">
<div class="block">
Java wrappers for interacting with external bioinformatics tools.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/blast2html/package-summary.html">org.biojava.bio.program.blast2html</a></td>
<td class="colLast">
<div class="block">Code for generating HTML reports from blast output</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/gff/package-summary.html">org.biojava.bio.program.gff</a></td>
<td class="colLast">
<div class="block">GFF manipulation.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/gff3/package-summary.html">org.biojava.bio.program.gff3</a></td>
<td class="colLast">
<div class="block">
Support for reading and writing GFF3.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/hmmer/package-summary.html">org.biojava.bio.program.hmmer</a></td>
<td class="colLast">
<div class="block">
Tools for working with profile Hidden Markov Models from the HMMer package.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/phred/package-summary.html">org.biojava.bio.program.phred</a></td>
<td class="colLast">
<div class="block">Parser for Phred output</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/sax/package-summary.html">org.biojava.bio.program.sax</a></td>
<td class="colLast">
<div class="block">Parsers which offer XML representations of the output from common
bioinformatics tools.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/sax/blastxml/package-summary.html">org.biojava.bio.program.sax.blastxml</a></td>
<td class="colLast">
<div class="block">
Parsers for the XML output from NCBI blast.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/ssbind/package-summary.html">org.biojava.bio.program.ssbind</a></td>
<td class="colLast">
<div class="block">
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/xml/package-summary.html">org.biojava.bio.program.xml</a></td>
<td class="colLast">
<div class="block">Utility classes for the <code>org.biojava.bio.program.sax</code>
package.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Dynamic programming packages table, listing packages, and an explanation">
<caption><span>Dynamic programming packages</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/dp/package-summary.html">org.biojava.bio.dp</a></td>
<td class="colLast">
<div class="block">HMM and Dynamic Programming Algorithms.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/dp/onehead/package-summary.html">org.biojava.bio.dp.onehead</a></td>
<td class="colLast">&nbsp;</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/dp/twohead/package-summary.html">org.biojava.bio.dp.twohead</a></td>
<td class="colLast">&nbsp;</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Chromatogram and trace file support table, listing packages, and an explanation">
<caption><span>Chromatogram and trace file support</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/chromatogram/package-summary.html">org.biojava.bio.chromatogram</a></td>
<td class="colLast">
<div class="block">
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/chromatogram/graphic/package-summary.html">org.biojava.bio.chromatogram.graphic</a></td>
<td class="colLast">
<div class="block">
Tools for displaying chromatograms.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/abi/package-summary.html">org.biojava.bio.program.abi</a></td>
<td class="colLast">
<div class="block">ABI Trace Handling.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/scf/package-summary.html">org.biojava.bio.program.scf</a></td>
<td class="colLast">
<div class="block">
Support for the SCF chromatogram format.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Macromolecular structure (PDB) table, listing packages, and an explanation">
<caption><span>Macromolecular structure (PDB)</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/das/dasstructure/package-summary.html">org.biojava.bio.program.das.dasstructure</a></td>
<td class="colLast">
<div class="block">
request a protein structure via DAS</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/structure/package-summary.html">org.biojava.bio.structure</a></td>
<td class="colLast">
<div class="block">
Interfaces and classes for protein structure (PDB).</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/structure/align/package-summary.html">org.biojava.bio.structure.align</a></td>
<td class="colLast">
<div class="block">Classes for the super-imposition of structures.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/structure/align/helper/package-summary.html">org.biojava.bio.structure.align.helper</a></td>
<td class="colLast">
<div class="block">Helper classes for structural alignment.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/structure/align/pairwise/package-summary.html">org.biojava.bio.structure.align.pairwise</a></td>
<td class="colLast">
<div class="block">Classes for the pairwise alignment of structures.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/structure/gui/package-summary.html">org.biojava.bio.structure.gui</a></td>
<td class="colLast">
<div class="block">
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.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/structure/io/package-summary.html">org.biojava.bio.structure.io</a></td>
<td class="colLast">
<div class="block">Input and Output of Structures</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/structure/jama/package-summary.html">org.biojava.bio.structure.jama</a></td>
<td class="colLast">
<div class="block">Matrix package for from <a href="http://math.nist.gov/javanumerics/jama/">JAMA</a></div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/structure/server/package-summary.html">org.biojava.bio.structure.server</a></td>
<td class="colLast">
<div class="block">
classes for easier management of PDB installations</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Utilities and developers' packages table, listing packages, and an explanation">
<caption><span>Utilities and developers' packages</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/tagvalue/package-summary.html">org.biojava.bio.program.tagvalue</a></td>
<td class="colLast">
<div class="block"> Process files as streams of records, each with tags with values.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/impl/package-summary.html">org.biojava.bio.seq.impl</a></td>
<td class="colLast">
<div class="block">Standard in-memory implementations of <code>Sequence</code> and
<code>Feature</code>.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/seq/io/filterxml/package-summary.html">org.biojava.bio.seq.io.filterxml</a></td>
<td class="colLast">
<div class="block">Tools for reading and writing an XML representation of BioJava's FeatureFilter language.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/projection/package-summary.html">org.biojava.bio.seq.projection</a></td>
<td class="colLast">
<div class="block">Code for projecting Feature objects and systematically altering their
properties.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/naming/package-summary.html">org.biojava.naming</a></td>
<td class="colLast">&nbsp;</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/ontology/package-summary.html">org.biojava.ontology</a></td>
<td class="colLast">
<div class="block">
A general-purpose API for ontologies.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/ontology/io/package-summary.html">org.biojava.ontology.io</a></td>
<td class="colLast">
<div class="block">
Tools for loading and saving ontologies.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/utils/package-summary.html">org.biojava.utils</a></td>
<td class="colLast">
<div class="block">
Miscellaneous utility classes used by other BioJava components.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/utils/automata/package-summary.html">org.biojava.utils.automata</a></td>
<td class="colLast">&nbsp;</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/utils/cache/package-summary.html">org.biojava.utils.cache</a></td>
<td class="colLast">
<div class="block">A simple cache system with pluggable caching behaviours.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/utils/candy/package-summary.html">org.biojava.utils.candy</a></td>
<td class="colLast">
<div class="block">The data structures and interfaces included in this package define an
interoperable framework for simple controlled vocabularies.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/utils/io/package-summary.html">org.biojava.utils.io</a></td>
<td class="colLast">
<div class="block">I/O utility classes.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/utils/math/package-summary.html">org.biojava.utils.math</a></td>
<td class="colLast">
<div class="block">
Mathematical utility classes.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/utils/net/package-summary.html">org.biojava.utils.net</a></td>
<td class="colLast">
<div class="block">
Network programming utility classes.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/utils/process/package-summary.html">org.biojava.utils.process</a></td>
<td class="colLast">
<div class="block">Classes and interfaces to execute external processes and to handle its input and output streams in multiple threads.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/utils/regex/package-summary.html">org.biojava.utils.regex</a></td>
<td class="colLast">
<div class="block">This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/utils/stax/package-summary.html">org.biojava.utils.stax</a></td>
<td class="colLast">
<div class="block">The Stack API for XML (StAX).</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/utils/walker/package-summary.html">org.biojava.utils.walker</a></td>
<td class="colLast">&nbsp;</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/utils/xml/package-summary.html">org.biojava.utils.xml</a></td>
<td class="colLast">
<div class="block">
Utility classes for handling and generating XML documents.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Molecular biology packages table, listing packages, and an explanation">
<caption><span>Molecular biology packages</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/molbio/package-summary.html">org.biojava.bio.molbio</a></td>
<td class="colLast">
<div class="block">The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/proteomics/package-summary.html">org.biojava.bio.proteomics</a></td>
<td class="colLast">
<div class="block">Utilities to aid in performing various physical analysis of proteins.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/proteomics/aaindex/package-summary.html">org.biojava.bio.proteomics.aaindex</a></td>
<td class="colLast">
<div class="block">Classes and interfaces to load Amino Acid Index database files.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Experimental packages table, listing packages, and an explanation">
<caption><span>Experimental packages</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/annodb/package-summary.html">org.biojava.bio.annodb</a></td>
<td class="colLast">
<div class="block">
Databases of generic structured data (annotation) objects.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/formats/package-summary.html">org.biojava.bio.program.formats</a></td>
<td class="colLast">
<div class="block">
Experimental parsers using the tagvalue framework.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/ssaha/package-summary.html">org.biojava.bio.program.ssaha</a></td>
<td class="colLast">
<div class="block">SSAHA sequence searching API.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/program/unigene/package-summary.html">org.biojava.bio.program.unigene</a></td>
<td class="colLast">
<div class="block">Objects for representing Unigene clusters.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/seq/distributed/package-summary.html">org.biojava.bio.seq.distributed</a></td>
<td class="colLast">
<div class="block">Sequences and SequenceDBs which are composed from data taken
from a number of data sources.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/seq/homol/package-summary.html">org.biojava.bio.seq.homol</a></td>
<td class="colLast">
<div class="block">The classes and interfaces for defining sequence similarity and
honology.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/stats/svm/package-summary.html">org.biojava.stats.svm</a></td>
<td class="colLast">
<div class="block">
Support Vector Machine classification and regression.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/stats/svm/tools/package-summary.html">org.biojava.stats.svm.tools</a></td>
<td class="colLast">
<div class="block">Tools for use of the SVM package.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/utils/lsid/package-summary.html">org.biojava.utils.lsid</a></td>
<td class="colLast">
<div class="block">Life Science Identifier (LSID) package.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Biojava extension (biojavax) packages table, listing packages, and an explanation">
<caption><span>Biojava extension (biojavax) packages</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/package-summary.html">org.biojavax</a></td>
<td class="colLast">
<div class="block">The Biojava extensions packages, classes that extend the core biojava 
     functionality</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojavax/bio/package-summary.html">org.biojavax.bio</a></td>
<td class="colLast">
<div class="block">Classes to represent biological entities and their relationships.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/bio/db/package-summary.html">org.biojavax.bio.db</a></td>
<td class="colLast">
<div class="block">Interactions between biojavax objects and a DB.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojavax/bio/db/biosql/package-summary.html">org.biojavax.bio.db.biosql</a></td>
<td class="colLast">
<div class="block">Interface between biojava and biosql databases</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/bio/db/ncbi/package-summary.html">org.biojavax.bio.db.ncbi</a></td>
<td class="colLast">
<div class="block">Interfaces to NCBI data.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojavax/bio/seq/package-summary.html">org.biojavax.bio.seq</a></td>
<td class="colLast">
<div class="block">Rich implementations of Sequences, Locations and Features.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/bio/seq/io/package-summary.html">org.biojavax.bio.seq.io</a></td>
<td class="colLast">
<div class="block">Classes to support the I/O of RichSequence and 
     Bioentry objects.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojavax/bio/taxa/package-summary.html">org.biojavax.bio.taxa</a></td>
<td class="colLast">
<div class="block">Objects that model the NCBI taxonomy schema as described in the BioSQL
  schema.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/bio/taxa/io/package-summary.html">org.biojavax.bio.taxa.io</a></td>
<td class="colLast">&nbsp;</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojavax/ontology/package-summary.html">org.biojavax.ontology</a></td>
<td class="colLast">
<div class="block">Extensions to the biojava ontology model that represent BioSQL ontology.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/utils/package-summary.html">org.biojavax.utils</a></td>
<td class="colLast">
<div class="block">Utility classes that are used by biojavax objects but could have wider utility
  to other applications.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Genetic Algorithm Framework table, listing packages, and an explanation">
<caption><span>Genetic Algorithm Framework</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/ga/package-summary.html">org.biojavax.ga</a></td>
<td class="colLast">
<div class="block">Classes to provide a genetic algorithm framework</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojavax/ga/exception/package-summary.html">org.biojavax.ga.exception</a></td>
<td class="colLast">
<div class="block">Exceptions related to the GA framework</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/ga/functions/package-summary.html">org.biojavax.ga.functions</a></td>
<td class="colLast">
<div class="block">GA functions</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojavax/ga/impl/package-summary.html">org.biojavax.ga.impl</a></td>
<td class="colLast">
<div class="block">Default implementations and abstract classes.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/ga/util/package-summary.html">org.biojavax.ga.util</a></td>
<td class="colLast">
<div class="block">Utility functions and helper classes</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Experimental Phylogeny packages table, listing packages, and an explanation">
<caption><span>Experimental Phylogeny packages</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojavax/bio/phylo/package-summary.html">org.biojavax.bio.phylo</a></td>
<td class="colLast">
<div class="block">Classes to support phlylogeny objects.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojavax/bio/phylo/io/phylip/package-summary.html">org.biojavax.bio.phylo.io.phylip</a></td>
<td class="colLast">
<div class="block">Classes to support the reading and writing of PHYLIP format.</div>
</td>
</tr>
</tbody>
</table>
</div>
<div class="contentContainer">
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Other Packages table, listing packages, and an explanation">
<caption><span>Other Packages</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/program/fastq/package-summary.html">org.biojava.bio.program.fastq</a></td>
<td class="colLast">
<div class="block">FASTQ and variants sequence format IO.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/structure/gui/events/package-summary.html">org.biojava.bio.structure.gui.events</a></td>
<td class="colLast">
<div class="block">
Some event classes for the protein structure GUIs.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/structure/gui/util/package-summary.html">org.biojava.bio.structure.gui.util</a></td>
<td class="colLast">
<div class="block">
Some utility classes for the protein structure GUIs.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/structure/io/mmcif/package-summary.html">org.biojava.bio.structure.io.mmcif</a></td>
<td class="colLast">
<div class="block">Input and Output of mmcif files</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/bio/structure/io/mmcif/chem/package-summary.html">org.biojava.bio.structure.io.mmcif.chem</a></td>
<td class="colLast">&nbsp;</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><a href="org/biojava/bio/structure/io/mmcif/model/package-summary.html">org.biojava.bio.structure.io.mmcif.model</a></td>
<td class="colLast">
<div class="block">Datamodel objects used for processing mmcif files.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><a href="org/biojava/ontology/obo/package-summary.html">org.biojava.ontology.obo</a></td>
<td class="colLast">&nbsp;</td>
</tr>
</tbody>
</table>
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