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<!DOCTYPE HTML>
<!-- NewPage -->
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<!-- Generated by javadoc (11.0.16) on Fri Oct 28 16:15:48 PDT 2022 -->
<title>Overview (biojava 6.1.0 API)</title>
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<h1 class="title">biojava 6.1.0 API</h1>
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<table class="overviewSummary">
<caption><span>Packages</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Package</th>
<th class="colLast" scope="col">Description</th>
</tr>
<tbody>
<tr class="altColor" id="i0">
<th class="colFirst" scope="row"><a href="demo/package-summary.html">demo</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i1">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/aaproperties/package-summary.html">org.biojava.nbio.aaproperties</a></th>
<td class="colLast">
<div class="block">Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.</div>
</td>
</tr>
<tr class="altColor" id="i2">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/aaproperties/profeat/package-summary.html">org.biojava.nbio.aaproperties.profeat</a></th>
<td class="colLast">
<div class="block">Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.</div>
</td>
</tr>
<tr class="rowColor" id="i3">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/aaproperties/profeat/convertor/package-summary.html">org.biojava.nbio.aaproperties.profeat.convertor</a></th>
<td class="colLast">
<div class="block">Set of classes that enable the conversion protein sequences into various attributes.</div>
</td>
</tr>
<tr class="altColor" id="i4">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/aaproperties/xml/package-summary.html">org.biojava.nbio.aaproperties.xml</a></th>
<td class="colLast">
<div class="block">Set of classes that handles the reading and writing of xml files.</div>
</td>
</tr>
<tr class="rowColor" id="i5">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/alignment/package-summary.html">org.biojava.nbio.alignment</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i6">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/alignment/io/package-summary.html">org.biojava.nbio.alignment.io</a></th>
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<tr class="rowColor" id="i7">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/alignment/routines/package-summary.html">org.biojava.nbio.alignment.routines</a></th>
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<tr class="altColor" id="i8">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/alignment/template/package-summary.html">org.biojava.nbio.alignment.template</a></th>
<td class="colLast"> </td>
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<tr class="rowColor" id="i9">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/alignment/package-summary.html">org.biojava.nbio.core.alignment</a></th>
<td class="colLast"> </td>
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<tr class="altColor" id="i10">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/alignment/matrices/package-summary.html">org.biojava.nbio.core.alignment.matrices</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i11">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/alignment/template/package-summary.html">org.biojava.nbio.core.alignment.template</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i12">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/exceptions/package-summary.html">org.biojava.nbio.core.exceptions</a></th>
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<tr class="rowColor" id="i13">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/search/io/package-summary.html">org.biojava.nbio.core.search.io</a></th>
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<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/search/io/blast/package-summary.html">org.biojava.nbio.core.search.io.blast</a></th>
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</tr>
<tr class="rowColor" id="i15">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/package-summary.html">org.biojava.nbio.core.sequence</a></th>
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<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/compound/package-summary.html">org.biojava.nbio.core.sequence.compound</a></th>
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<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/edits/package-summary.html">org.biojava.nbio.core.sequence.edits</a></th>
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<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/features/package-summary.html">org.biojava.nbio.core.sequence.features</a></th>
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<tr class="rowColor" id="i19">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/io/package-summary.html">org.biojava.nbio.core.sequence.io</a></th>
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<tr class="altColor" id="i20">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/io/embl/package-summary.html">org.biojava.nbio.core.sequence.io.embl</a></th>
<td class="colLast"> </td>
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<tr class="rowColor" id="i21">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/io/template/package-summary.html">org.biojava.nbio.core.sequence.io.template</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i22">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/io/util/package-summary.html">org.biojava.nbio.core.sequence.io.util</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i23">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/loader/package-summary.html">org.biojava.nbio.core.sequence.loader</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i24">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/location/package-summary.html">org.biojava.nbio.core.sequence.location</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i25">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/location/template/package-summary.html">org.biojava.nbio.core.sequence.location.template</a></th>
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</tr>
<tr class="altColor" id="i26">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/reference/package-summary.html">org.biojava.nbio.core.sequence.reference</a></th>
<td class="colLast"> </td>
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<tr class="rowColor" id="i27">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/storage/package-summary.html">org.biojava.nbio.core.sequence.storage</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i28">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/template/package-summary.html">org.biojava.nbio.core.sequence.template</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i29">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/transcription/package-summary.html">org.biojava.nbio.core.sequence.transcription</a></th>
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</tr>
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<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/sequence/views/package-summary.html">org.biojava.nbio.core.sequence.views</a></th>
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<tr class="rowColor" id="i31">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/core/util/package-summary.html">org.biojava.nbio.core.util</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i32">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/data/sequence/package-summary.html">org.biojava.nbio.data.sequence</a></th>
<td class="colLast">
<div class="block">Set of classes that responsible for data handling.</div>
</td>
</tr>
<tr class="rowColor" id="i33">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/package-summary.html">org.biojava.nbio.genome</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i34">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/homology/package-summary.html">org.biojava.nbio.genome.homology</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i35">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/io/fastq/package-summary.html">org.biojava.nbio.genome.io.fastq</a></th>
<td class="colLast">
<div class="block">FASTQ and variants sequence format I/O.</div>
</td>
</tr>
<tr class="altColor" id="i36">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/parsers/cytoband/package-summary.html">org.biojava.nbio.genome.parsers.cytoband</a></th>
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</tr>
<tr class="rowColor" id="i37">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/parsers/geneid/package-summary.html">org.biojava.nbio.genome.parsers.geneid</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i38">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/parsers/genename/package-summary.html">org.biojava.nbio.genome.parsers.genename</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i39">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/parsers/gff/package-summary.html">org.biojava.nbio.genome.parsers.gff</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i40">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/parsers/twobit/package-summary.html">org.biojava.nbio.genome.parsers.twobit</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i41">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/query/package-summary.html">org.biojava.nbio.genome.query</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i42">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/uniprot/package-summary.html">org.biojava.nbio.genome.uniprot</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i43">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/genome/util/package-summary.html">org.biojava.nbio.genome.util</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i44">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/ontology/package-summary.html">org.biojava.nbio.ontology</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i45">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/ontology/io/package-summary.html">org.biojava.nbio.ontology.io</a></th>
</tr>
<tr class="altColor" id="i46">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/ontology/obo/package-summary.html">org.biojava.nbio.ontology.obo</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i47">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/ontology/utils/package-summary.html">org.biojava.nbio.ontology.utils</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i48">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/phosphosite/package-summary.html">org.biojava.nbio.phosphosite</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i49">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/phylo/package-summary.html">org.biojava.nbio.phylo</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i50">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/proteincomparisontool/package-summary.html">org.biojava.nbio.proteincomparisontool</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i51">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/protmod/package-summary.html">org.biojava.nbio.protmod</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i52">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/protmod/io/package-summary.html">org.biojava.nbio.protmod.io</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i53">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/protmod/structure/package-summary.html">org.biojava.nbio.protmod.structure</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i54">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/ronn/package-summary.html">org.biojava.nbio.ronn</a></th>
<td class="colLast">
<div class="block">
BioJava provide a module biojava-protein-disorder for prediction disordered regions
from a protein sequence.</div>
</td>
</tr>
<tr class="rowColor" id="i55">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/package-summary.html">org.biojava.nbio.structure</a></th>
</tr>
<tr class="altColor" id="i56">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/package-summary.html">org.biojava.nbio.structure.align</a></th>
<td class="colLast">
<div class="block">Classes for the alignment of structures.</div>
</td>
</tr>
<tr class="rowColor" id="i57">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/ce/package-summary.html">org.biojava.nbio.structure.align.ce</a></th>
<td class="colLast">
<div class="block">Classes related to the implementation of the CE alignment algorithm, here called jCE.</div>
</td>
</tr>
<tr class="altColor" id="i58">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/client/package-summary.html">org.biojava.nbio.structure.align.client</a></th>
<td class="colLast">
<div class="block">This package deals with the server communication for auto-downloading pre-calculated alignments.</div>
</td>
</tr>
<tr class="rowColor" id="i59">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/fatcat/package-summary.html">org.biojava.nbio.structure.align.fatcat</a></th>
<td class="colLast">
<div class="block">Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.</div>
</td>
</tr>
<tr class="altColor" id="i60">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/fatcat/calc/package-summary.html">org.biojava.nbio.structure.align.fatcat.calc</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i61">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/gui/package-summary.html">org.biojava.nbio.structure.align.gui</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i62">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/gui/aligpanel/package-summary.html">org.biojava.nbio.structure.align.gui.aligpanel</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i63">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/gui/autosuggest/package-summary.html">org.biojava.nbio.structure.align.gui.autosuggest</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i64">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/gui/jmol/package-summary.html">org.biojava.nbio.structure.align.gui.jmol</a></th>
<td class="colLast">
<div class="block">Utility methods for better interaction with Jmol.</div>
</td>
</tr>
<tr class="rowColor" id="i65">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/helper/package-summary.html">org.biojava.nbio.structure.align.helper</a></th>
<td class="colLast">
<div class="block">Helper classes for structural alignment.</div>
</td>
</tr>
<tr class="altColor" id="i66">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/model/package-summary.html">org.biojava.nbio.structure.align.model</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i67">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/multiple/package-summary.html">org.biojava.nbio.structure.align.multiple</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i68">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/multiple/mc/package-summary.html">org.biojava.nbio.structure.align.multiple.mc</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i69">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/multiple/util/package-summary.html">org.biojava.nbio.structure.align.multiple.util</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i70">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/pairwise/package-summary.html">org.biojava.nbio.structure.align.pairwise</a></th>
<td class="colLast">
<div class="block">Classes for the pairwise alignment of structures.</div>
</td>
</tr>
<tr class="rowColor" id="i71">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/quaternary/package-summary.html">org.biojava.nbio.structure.align.quaternary</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i72">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/seq/package-summary.html">org.biojava.nbio.structure.align.seq</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i73">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/util/package-summary.html">org.biojava.nbio.structure.align.util</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i74">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/webstart/package-summary.html">org.biojava.nbio.structure.align.webstart</a></th>
<td class="colLast">
<div class="block">Classes related to Java Web Start</div>
</td>
</tr>
<tr class="rowColor" id="i75">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/align/xml/package-summary.html">org.biojava.nbio.structure.align.xml</a></th>
<td class="colLast">
<div class="block">Serialization and deserialization for structure alignment results (as AFPChain object) to XML.</div>
</td>
</tr>
<tr class="altColor" id="i76">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/asa/package-summary.html">org.biojava.nbio.structure.asa</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i77">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/basepairs/package-summary.html">org.biojava.nbio.structure.basepairs</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i78">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/cath/package-summary.html">org.biojava.nbio.structure.cath</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i79">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/chem/package-summary.html">org.biojava.nbio.structure.chem</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i80">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/cluster/package-summary.html">org.biojava.nbio.structure.cluster</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i81">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/contact/package-summary.html">org.biojava.nbio.structure.contact</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i82">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/domain/package-summary.html">org.biojava.nbio.structure.domain</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i83">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/domain/pdp/package-summary.html">org.biojava.nbio.structure.domain.pdp</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i84">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/ecod/package-summary.html">org.biojava.nbio.structure.ecod</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i85">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/geometry/package-summary.html">org.biojava.nbio.structure.geometry</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i86">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/gui/package-summary.html">org.biojava.nbio.structure.gui</a></th>
</tr>
<tr class="rowColor" id="i87">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/gui/events/package-summary.html">org.biojava.nbio.structure.gui.events</a></th>
</tr>
<tr class="altColor" id="i88">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/gui/util/package-summary.html">org.biojava.nbio.structure.gui.util</a></th>
</tr>
<tr class="rowColor" id="i89">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/gui/util/color/package-summary.html">org.biojava.nbio.structure.gui.util.color</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i90">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/io/package-summary.html">org.biojava.nbio.structure.io</a></th>
<td class="colLast">
<div class="block">Input and Output of Structures</div>
</td>
</tr>
<tr class="rowColor" id="i91">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/io/cif/package-summary.html">org.biojava.nbio.structure.io.cif</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i92">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/io/mmtf/package-summary.html">org.biojava.nbio.structure.io.mmtf</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i93">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/io/sifts/package-summary.html">org.biojava.nbio.structure.io.sifts</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i94">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/io/util/package-summary.html">org.biojava.nbio.structure.io.util</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i95">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/jama/package-summary.html">org.biojava.nbio.structure.jama</a></th>
<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" id="i96">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/math/package-summary.html">org.biojava.nbio.structure.math</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i97">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/quaternary/package-summary.html">org.biojava.nbio.structure.quaternary</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i98">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/scop/package-summary.html">org.biojava.nbio.structure.scop</a></th>
<td class="colLast">
<div class="block">Parsers and API for <a href="http://scop.mrc-lmb.cam.ac.uk/scop/">SCOP, Structural Classification of Proteins</a>.</div>
</td>
</tr>
<tr class="rowColor" id="i99">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/secstruc/package-summary.html">org.biojava.nbio.structure.secstruc</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i100">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/symmetry/axis/package-summary.html">org.biojava.nbio.structure.symmetry.axis</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i101">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/symmetry/core/package-summary.html">org.biojava.nbio.structure.symmetry.core</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i102">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/symmetry/geometry/package-summary.html">org.biojava.nbio.structure.symmetry.geometry</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i103">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/symmetry/gui/package-summary.html">org.biojava.nbio.structure.symmetry.gui</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i104">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/symmetry/internal/package-summary.html">org.biojava.nbio.structure.symmetry.internal</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i105">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/symmetry/jmolScript/package-summary.html">org.biojava.nbio.structure.symmetry.jmolScript</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i106">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/symmetry/misc/package-summary.html">org.biojava.nbio.structure.symmetry.misc</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i107">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/symmetry/utils/package-summary.html">org.biojava.nbio.structure.symmetry.utils</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i108">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/xtal/package-summary.html">org.biojava.nbio.structure.xtal</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i109">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/structure/xtal/io/package-summary.html">org.biojava.nbio.structure.xtal.io</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i110">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/survival/cox/package-summary.html">org.biojava.nbio.survival.cox</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i111">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/survival/cox/comparators/package-summary.html">org.biojava.nbio.survival.cox.comparators</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i112">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/survival/cox/matrix/package-summary.html">org.biojava.nbio.survival.cox.matrix</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i113">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/survival/cox/stats/package-summary.html">org.biojava.nbio.survival.cox.stats</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i114">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/survival/data/package-summary.html">org.biojava.nbio.survival.data</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i115">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/survival/kaplanmeier/figure/package-summary.html">org.biojava.nbio.survival.kaplanmeier.figure</a></th>
<td class="colLast"> </td>
</tr>
<tr class="altColor" id="i116">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/survival/kaplanmeier/metadata/package-summary.html">org.biojava.nbio.survival.kaplanmeier.metadata</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i117">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/ws/alignment/package-summary.html">org.biojava.nbio.ws.alignment</a></th>
<td class="colLast">
<div class="block">This package contains the interfaces that need to be implemented by discrete alignment services.</div>
</td>
</tr>
<tr class="altColor" id="i118">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/ws/alignment/qblast/package-summary.html">org.biojava.nbio.ws.alignment.qblast</a></th>
<td class="colLast"> </td>
</tr>
<tr class="rowColor" id="i119">
<th class="colFirst" scope="row"><a href="org/biojava/nbio/ws/hmmer/package-summary.html">org.biojava.nbio.ws.hmmer</a></th>
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