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  95 <li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
  96 <li class="toctree-l1 current"><a class="current reference internal" href="#">Included Tools</a><ul>
  97 <li class="toctree-l2"><a class="reference internal" href="#multiple-sequence-alignment">Multiple Sequence Alignment</a></li>
  98 <li class="toctree-l2"><a class="reference internal" href="#protein-disorder-prediction">Protein Disorder Prediction</a></li>
  99 <li class="toctree-l2"><a class="reference internal" href="#amino-acid-conservation">Amino Acid Conservation</a></li>
 100 <li class="toctree-l2"><a class="reference internal" href="#rna-secondary-structure">RNA Secondary Structure</a></li>
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 175   <div class="section" id="included-tools">
 176 <h1>Included Tools<a class="headerlink" href="#included-tools" title="Permalink to this headline">¶</a></h1>
 177 <div class="section" id="multiple-sequence-alignment">
 178 <span id="msa"></span><h2>Multiple Sequence Alignment<a class="headerlink" href="#multiple-sequence-alignment" title="Permalink to this headline">¶</a></h2>
 179 <ul class="simple">
 180 <li><a class="reference external" href="http://www.clustal.org/omega">Clustal Omega</a> (version 1.2.4)</li>
 181 <li><a class="reference external" href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.1)</li>
 182 <li><a class="reference external" href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 7.310)</li>
 183 <li><a class="reference external" href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31)</li>
 184 <li><a class="reference external" href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-coffee</a> (version 11.00.8cbe486)</li>
 185 <li><a class="reference external" href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
 186 <li><a class="reference external" href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>
 187 <li><a class="reference external" href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</li>
 188 </ul>
 189 </div>
 190 <div class="section" id="protein-disorder-prediction">
 191 <span id="pdis"></span><h2>Protein Disorder Prediction<a class="headerlink" href="#protein-disorder-prediction" title="Permalink to this headline">¶</a></h2>
 192 <ul class="simple">
 193 <li><a class="reference external" href="http://dis.embl.de/">DisEMBL</a> (version 1.5)</li>
 194 <li><a class="reference external" href="http://iupred.enzim.hu">IUPred</a> (version 1.0)</li>
 195 <li>Jronn - Java implementation of <a class="reference external" href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> (version 3.1)</li>
 196 <li><a class="reference external" href="http://globplot.embl.de/">GlobPlot</a> (version 2.3)</li>
 197 </ul>
 198 </div>
 199 <div class="section" id="amino-acid-conservation">
 200 <span id="aac"></span><h2>Amino Acid Conservation<a class="headerlink" href="#amino-acid-conservation" title="Permalink to this headline">¶</a></h2>
 201 <ul class="simple">
 202 <li><a class="reference external" href="http://www.compbio.dundee.ac.uk/aacon">AACon</a> (version 1.1)</li>
 203 </ul>
 204 </div>
 205 <div class="section" id="rna-secondary-structure">
 206 <span id="rnass"></span><h2>RNA Secondary Structure<a class="headerlink" href="#rna-secondary-structure" title="Permalink to this headline">¶</a></h2>
 207 <ul class="simple">
 208 <li>RNAalifold from <a class="reference external" href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a> (version 2.0)</li>
 209 </ul>
 210 </div>
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