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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_03-Ubuntu) on Tue May 03 16:45:05 PDT 2016 -->
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>Overview List (biojava 4.2.1 API)</title>
<meta name="date" content="2016-05-03">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
<script type="text/javascript" src="script.js"></script>
</head>
<body>
<div class="indexHeader"><span><a href="allclasses-frame.html" target="packageFrame">All Classes</a></span></div>
<div class="indexContainer">
<h2 title="Packages">Packages</h2>
<ul title="Packages">
<li><a href="demo/package-frame.html" target="packageFrame">demo</a></li>
<li><a href="org/biojava/nbio/aaproperties/package-frame.html" target="packageFrame">org.biojava.nbio.aaproperties</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/package-frame.html" target="packageFrame">org.biojava.nbio.aaproperties.profeat</a></li>
<li><a href="org/biojava/nbio/aaproperties/profeat/convertor/package-frame.html" target="packageFrame">org.biojava.nbio.aaproperties.profeat.convertor</a></li>
<li><a href="org/biojava/nbio/aaproperties/xml/package-frame.html" target="packageFrame">org.biojava.nbio.aaproperties.xml</a></li>
<li><a href="org/biojava/nbio/alignment/package-frame.html" target="packageFrame">org.biojava.nbio.alignment</a></li>
<li><a href="org/biojava/nbio/alignment/io/package-frame.html" target="packageFrame">org.biojava.nbio.alignment.io</a></li>
<li><a href="org/biojava/nbio/alignment/routines/package-frame.html" target="packageFrame">org.biojava.nbio.alignment.routines</a></li>
<li><a href="org/biojava/nbio/alignment/template/package-frame.html" target="packageFrame">org.biojava.nbio.alignment.template</a></li>
<li><a href="org/biojava/nbio/core/alignment/package-frame.html" target="packageFrame">org.biojava.nbio.core.alignment</a></li>
<li><a href="org/biojava/nbio/core/alignment/matrices/package-frame.html" target="packageFrame">org.biojava.nbio.core.alignment.matrices</a></li>
<li><a href="org/biojava/nbio/core/alignment/template/package-frame.html" target="packageFrame">org.biojava.nbio.core.alignment.template</a></li>
<li><a href="org/biojava/nbio/core/exceptions/package-frame.html" target="packageFrame">org.biojava.nbio.core.exceptions</a></li>
<li><a href="org/biojava/nbio/core/search/io/package-frame.html" target="packageFrame">org.biojava.nbio.core.search.io</a></li>
<li><a href="org/biojava/nbio/core/search/io/blast/package-frame.html" target="packageFrame">org.biojava.nbio.core.search.io.blast</a></li>
<li><a href="org/biojava/nbio/core/sequence/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence</a></li>
<li><a href="org/biojava/nbio/core/sequence/compound/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.compound</a></li>
<li><a href="org/biojava/nbio/core/sequence/edits/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.edits</a></li>
<li><a href="org/biojava/nbio/core/sequence/features/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.features</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.io</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/template/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.io.template</a></li>
<li><a href="org/biojava/nbio/core/sequence/io/util/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.io.util</a></li>
<li><a href="org/biojava/nbio/core/sequence/loader/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.loader</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.location</a></li>
<li><a href="org/biojava/nbio/core/sequence/location/template/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.location.template</a></li>
<li><a href="org/biojava/nbio/core/sequence/storage/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.storage</a></li>
<li><a href="org/biojava/nbio/core/sequence/template/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.template</a></li>
<li><a href="org/biojava/nbio/core/sequence/transcription/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.transcription</a></li>
<li><a href="org/biojava/nbio/core/sequence/views/package-frame.html" target="packageFrame">org.biojava.nbio.core.sequence.views</a></li>
<li><a href="org/biojava/nbio/core/util/package-frame.html" target="packageFrame">org.biojava.nbio.core.util</a></li>
<li><a href="org/biojava/nbio/data/sequence/package-frame.html" target="packageFrame">org.biojava.nbio.data.sequence</a></li>
<li><a href="org/biojava/nbio/genome/package-frame.html" target="packageFrame">org.biojava.nbio.genome</a></li>
<li><a href="org/biojava/nbio/genome/homology/package-frame.html" target="packageFrame">org.biojava.nbio.genome.homology</a></li>
<li><a href="org/biojava/nbio/genome/parsers/cytoband/package-frame.html" target="packageFrame">org.biojava.nbio.genome.parsers.cytoband</a></li>
<li><a href="org/biojava/nbio/genome/parsers/geneid/package-frame.html" target="packageFrame">org.biojava.nbio.genome.parsers.geneid</a></li>
<li><a href="org/biojava/nbio/genome/parsers/genename/package-frame.html" target="packageFrame">org.biojava.nbio.genome.parsers.genename</a></li>
<li><a href="org/biojava/nbio/genome/parsers/gff/package-frame.html" target="packageFrame">org.biojava.nbio.genome.parsers.gff</a></li>
<li><a href="org/biojava/nbio/genome/parsers/twobit/package-frame.html" target="packageFrame">org.biojava.nbio.genome.parsers.twobit</a></li>
<li><a href="org/biojava/nbio/genome/query/package-frame.html" target="packageFrame">org.biojava.nbio.genome.query</a></li>
<li><a href="org/biojava/nbio/genome/uniprot/package-frame.html" target="packageFrame">org.biojava.nbio.genome.uniprot</a></li>
<li><a href="org/biojava/nbio/genome/util/package-frame.html" target="packageFrame">org.biojava.nbio.genome.util</a></li>
<li><a href="org/biojava/nbio/ontology/package-frame.html" target="packageFrame">org.biojava.nbio.ontology</a></li>
<li><a href="org/biojava/nbio/ontology/io/package-frame.html" target="packageFrame">org.biojava.nbio.ontology.io</a></li>
<li><a href="org/biojava/nbio/ontology/obo/package-frame.html" target="packageFrame">org.biojava.nbio.ontology.obo</a></li>
<li><a href="org/biojava/nbio/ontology/utils/package-frame.html" target="packageFrame">org.biojava.nbio.ontology.utils</a></li>
<li><a href="org/biojava/nbio/phosphosite/package-frame.html" target="packageFrame">org.biojava.nbio.phosphosite</a></li>
<li><a href="org/biojava/nbio/phylo/package-frame.html" target="packageFrame">org.biojava.nbio.phylo</a></li>
<li><a href="org/biojava/nbio/protmod/package-frame.html" target="packageFrame">org.biojava.nbio.protmod</a></li>
<li><a href="org/biojava/nbio/protmod/io/package-frame.html" target="packageFrame">org.biojava.nbio.protmod.io</a></li>
<li><a href="org/biojava/nbio/protmod/structure/package-frame.html" target="packageFrame">org.biojava.nbio.protmod.structure</a></li>
<li><a href="org/biojava/nbio/ronn/package-frame.html" target="packageFrame">org.biojava.nbio.ronn</a></li>
<li><a href="org/biojava/nbio/sequencing/io/fastq/package-frame.html" target="packageFrame">org.biojava.nbio.sequencing.io.fastq</a></li>
<li><a href="org/biojava/nbio/structure/package-frame.html" target="packageFrame">org.biojava.nbio.structure</a></li>
<li><a href="org/biojava/nbio/structure/align/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align</a></li>
<li><a href="org/biojava/nbio/structure/align/ce/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.ce</a></li>
<li><a href="org/biojava/nbio/structure/align/client/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.client</a></li>
<li><a href="org/biojava/nbio/structure/align/events/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.events</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.fatcat</a></li>
<li><a href="org/biojava/nbio/structure/align/fatcat/calc/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.fatcat.calc</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.gui</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/aligpanel/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.gui.aligpanel</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/autosuggest/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.gui.autosuggest</a></li>
<li><a href="org/biojava/nbio/structure/align/gui/jmol/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.gui.jmol</a></li>
<li><a href="org/biojava/nbio/structure/align/helper/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.helper</a></li>
<li><a href="org/biojava/nbio/structure/align/model/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.model</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.multiple</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/mc/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.multiple.mc</a></li>
<li><a href="org/biojava/nbio/structure/align/multiple/util/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.multiple.util</a></li>
<li><a href="org/biojava/nbio/structure/align/pairwise/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.pairwise</a></li>
<li><a href="org/biojava/nbio/structure/align/seq/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.seq</a></li>
<li><a href="org/biojava/nbio/structure/align/util/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.util</a></li>
<li><a href="org/biojava/nbio/structure/align/webstart/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.webstart</a></li>
<li><a href="org/biojava/nbio/structure/align/xml/package-frame.html" target="packageFrame">org.biojava.nbio.structure.align.xml</a></li>
<li><a href="org/biojava/nbio/structure/asa/package-frame.html" target="packageFrame">org.biojava.nbio.structure.asa</a></li>
<li><a href="org/biojava/nbio/structure/cath/package-frame.html" target="packageFrame">org.biojava.nbio.structure.cath</a></li>
<li><a href="org/biojava/nbio/structure/contact/package-frame.html" target="packageFrame">org.biojava.nbio.structure.contact</a></li>
<li><a href="org/biojava/nbio/structure/domain/package-frame.html" target="packageFrame">org.biojava.nbio.structure.domain</a></li>
<li><a href="org/biojava/nbio/structure/domain/pdp/package-frame.html" target="packageFrame">org.biojava.nbio.structure.domain.pdp</a></li>
<li><a href="org/biojava/nbio/structure/ecod/package-frame.html" target="packageFrame">org.biojava.nbio.structure.ecod</a></li>
<li><a href="org/biojava/nbio/structure/gui/package-frame.html" target="packageFrame">org.biojava.nbio.structure.gui</a></li>
<li><a href="org/biojava/nbio/structure/gui/events/package-frame.html" target="packageFrame">org.biojava.nbio.structure.gui.events</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/package-frame.html" target="packageFrame">org.biojava.nbio.structure.gui.util</a></li>
<li><a href="org/biojava/nbio/structure/gui/util/color/package-frame.html" target="packageFrame">org.biojava.nbio.structure.gui.util.color</a></li>
<li><a href="org/biojava/nbio/structure/io/package-frame.html" target="packageFrame">org.biojava.nbio.structure.io</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/package-frame.html" target="packageFrame">org.biojava.nbio.structure.io.mmcif</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/chem/package-frame.html" target="packageFrame">org.biojava.nbio.structure.io.mmcif.chem</a></li>
<li><a href="org/biojava/nbio/structure/io/mmcif/model/package-frame.html" target="packageFrame">org.biojava.nbio.structure.io.mmcif.model</a></li>
<li><a href="org/biojava/nbio/structure/io/sifts/package-frame.html" target="packageFrame">org.biojava.nbio.structure.io.sifts</a></li>
<li><a href="org/biojava/nbio/structure/io/util/package-frame.html" target="packageFrame">org.biojava.nbio.structure.io.util</a></li>
<li><a href="org/biojava/nbio/structure/jama/package-frame.html" target="packageFrame">org.biojava.nbio.structure.jama</a></li>
<li><a href="org/biojava/nbio/structure/math/package-frame.html" target="packageFrame">org.biojava.nbio.structure.math</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/package-frame.html" target="packageFrame">org.biojava.nbio.structure.quaternary</a></li>
<li><a href="org/biojava/nbio/structure/quaternary/io/package-frame.html" target="packageFrame">org.biojava.nbio.structure.quaternary.io</a></li>
<li><a href="org/biojava/nbio/structure/rcsb/package-frame.html" target="packageFrame">org.biojava.nbio.structure.rcsb</a></li>
<li><a href="org/biojava/nbio/structure/scop/package-frame.html" target="packageFrame">org.biojava.nbio.structure.scop</a></li>
<li><a href="org/biojava/nbio/structure/scop/server/package-frame.html" target="packageFrame">org.biojava.nbio.structure.scop.server</a></li>
<li><a href="org/biojava/nbio/structure/secstruc/package-frame.html" target="packageFrame">org.biojava.nbio.structure.secstruc</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/analysis/package-frame.html" target="packageFrame">org.biojava.nbio.structure.symmetry.analysis</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/core/package-frame.html" target="packageFrame">org.biojava.nbio.structure.symmetry.core</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/geometry/package-frame.html" target="packageFrame">org.biojava.nbio.structure.symmetry.geometry</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/gui/package-frame.html" target="packageFrame">org.biojava.nbio.structure.symmetry.gui</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/internal/package-frame.html" target="packageFrame">org.biojava.nbio.structure.symmetry.internal</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/jmolScript/package-frame.html" target="packageFrame">org.biojava.nbio.structure.symmetry.jmolScript</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/misc/package-frame.html" target="packageFrame">org.biojava.nbio.structure.symmetry.misc</a></li>
<li><a href="org/biojava/nbio/structure/symmetry/utils/package-frame.html" target="packageFrame">org.biojava.nbio.structure.symmetry.utils</a></li>
<li><a href="org/biojava/nbio/structure/validation/package-frame.html" target="packageFrame">org.biojava.nbio.structure.validation</a></li>
<li><a href="org/biojava/nbio/structure/xtal/package-frame.html" target="packageFrame">org.biojava.nbio.structure.xtal</a></li>
<li><a href="org/biojava/nbio/structure/xtal/io/package-frame.html" target="packageFrame">org.biojava.nbio.structure.xtal.io</a></li>
<li><a href="org/biojava/nbio/survival/cox/package-frame.html" target="packageFrame">org.biojava.nbio.survival.cox</a></li>
<li><a href="org/biojava/nbio/survival/cox/comparators/package-frame.html" target="packageFrame">org.biojava.nbio.survival.cox.comparators</a></li>
<li><a href="org/biojava/nbio/survival/cox/matrix/package-frame.html" target="packageFrame">org.biojava.nbio.survival.cox.matrix</a></li>
<li><a href="org/biojava/nbio/survival/cox/stats/package-frame.html" target="packageFrame">org.biojava.nbio.survival.cox.stats</a></li>
<li><a href="org/biojava/nbio/survival/data/package-frame.html" target="packageFrame">org.biojava.nbio.survival.data</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/figure/package-frame.html" target="packageFrame">org.biojava.nbio.survival.kaplanmeier.figure</a></li>
<li><a href="org/biojava/nbio/survival/kaplanmeier/metadata/package-frame.html" target="packageFrame">org.biojava.nbio.survival.kaplanmeier.metadata</a></li>
<li><a href="org/biojava/nbio/ws/alignment/package-frame.html" target="packageFrame">org.biojava.nbio.ws.alignment</a></li>
<li><a href="org/biojava/nbio/ws/alignment/qblast/package-frame.html" target="packageFrame">org.biojava.nbio.ws.alignment.qblast</a></li>
<li><a href="org/biojava/nbio/ws/hmmer/package-frame.html" target="packageFrame">org.biojava.nbio.ws.hmmer</a></li>
</ul>
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