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  94 <li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
  95 <li class="toctree-l1"><a class="reference internal" href="included_tools.html">Included Tools</a></li>
  96 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a></li>
  97 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a></li>
  98 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a></li>
  99 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a></li>
 100 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a></li>
 101 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a></li>
 102 <li class="toctree-l1"><a class="reference internal" href="citations.html">Citations</a></li>
 103 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a></li>
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 168 <h1>Welcome to JABAWS&#8217;s documentation!<a class="headerlink" href="#welcome-to-jabaws-s-documentation" title="Permalink to this headline">¶</a></h1>
 169 <p>Read on these documentation pages or go back to the <a class="reference external" href="../">JABAWS homepage</a>!</p>
 170 <p>JABAWS documentation is also available in <em>pdf</em>. <a class="reference external" href="./jabaws_manual.pdf">Download it here</a>!</p>
 171 <div class="toctree-wrapper compound">
 172 <p class="caption"><span class="caption-text">Contents:</span></p>
 173 <ul>
 174 <li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a><ul>
 175 <li class="toctree-l2"><a class="reference internal" href="getting_started.html#jabaws-benefits">JABAWS Benefits</a></li>
 176 <li class="toctree-l2"><a class="reference internal" href="getting_started.html#jabaws-distributions">JABAWS Distributions</a><ul>
 177 <li class="toctree-l3"><a class="reference internal" href="getting_started.html#jalview-and-the-jabaws-public-server">Jalview and the JABAWS Public Server</a></li>
 178 <li class="toctree-l3"><a class="reference internal" href="getting_started.html#command-line-client-cli">Command Line Client (CLI)</a></li>
 179 <li class="toctree-l3"><a class="reference internal" href="getting_started.html#web-application-archive-war">Web Application aRchive (WAR)</a></li>
 180 <li class="toctree-l3"><a class="reference internal" href="getting_started.html#virtual-appliance-va">Virtual Appliance (VA)</a></li>
 181 </ul>
 182 </li>
 183 </ul>
 184 </li>
 185 <li class="toctree-l1"><a class="reference internal" href="included_tools.html">Included Tools</a><ul>
 186 <li class="toctree-l2"><a class="reference internal" href="included_tools.html#multiple-sequence-alignment">Multiple Sequence Alignment</a></li>
 187 <li class="toctree-l2"><a class="reference internal" href="included_tools.html#protein-disorder-prediction">Protein Disorder Prediction</a></li>
 188 <li class="toctree-l2"><a class="reference internal" href="included_tools.html#amino-acid-conservation">Amino Acid Conservation</a></li>
 189 <li class="toctree-l2"><a class="reference internal" href="included_tools.html#rna-secondary-structure">RNA Secondary Structure</a></li>
 190 </ul>
 191 </li>
 192 <li class="toctree-l1"><a class="reference internal" href="client.html">Command Line Client (CLI)</a><ul>
 193 <li class="toctree-l2"><a class="reference internal" href="client.html#installing">Installing</a></li>
 194 <li class="toctree-l2"><a class="reference internal" href="client.html#usage">Usage</a></li>
 195 <li class="toctree-l2"><a class="reference internal" href="client.html#example-usage">Example Usage</a></li>
 196 </ul>
 197 </li>
 198 <li class="toctree-l1"><a class="reference internal" href="war.html">Web Application Archive (WAR)</a><ul>
 199 <li class="toctree-l2"><a class="reference internal" href="war.html#installing">Installing</a></li>
 200 <li class="toctree-l2"><a class="reference internal" href="war.html#usage">Usage</a></li>
 201 <li class="toctree-l2"><a class="reference internal" href="war.html#troubleshooting">Troubleshooting</a></li>
 202 </ul>
 203 </li>
 204 <li class="toctree-l1"><a class="reference internal" href="va.html">Virtual Appliance (VA)</a><ul>
 205 <li class="toctree-l2"><a class="reference internal" href="va.html#installing">Installing</a></li>
 206 <li class="toctree-l2"><a class="reference internal" href="va.html#usage">Usage</a></li>
 207 <li class="toctree-l2"><a class="reference internal" href="va.html#configuration">Configuration</a><ul>
 208 <li class="toctree-l3"><a class="reference internal" href="va.html#vm-configuration">VM configuration</a></li>
 209 <li class="toctree-l3"><a class="reference internal" href="va.html#jabaws-configuration">JABAWS configuration</a></li>
 210 </ul>
 211 </li>
 212 </ul>
 213 </li>
 214 <li class="toctree-l1"><a class="reference internal" href="advanced.html">Advanced Usage</a><ul>
 215 <li class="toctree-l2"><a class="reference internal" href="advanced.html#valid-wsdl">Valid WSDL</a></li>
 216 <li class="toctree-l2"><a class="reference internal" href="advanced.html#jabaws-configuration">JABAWS Configuration</a><ul>
 217 <li class="toctree-l3"><a class="reference internal" href="advanced.html#local-engine-configuration">Local Engine Configuration</a></li>
 218 <li class="toctree-l3"><a class="reference internal" href="advanced.html#cluster-engine-configuration">Cluster Engine Configuration</a></li>
 219 <li class="toctree-l3"><a class="reference internal" href="advanced.html#executable-configuration">Executable Configuration</a></li>
 220 <li class="toctree-l3"><a class="reference internal" href="advanced.html#defining-environment-variables-for-executables">Defining Environment Variables for Executables</a></li>
 221 <li class="toctree-l3"><a class="reference internal" href="advanced.html#configure-jabaws-to-work-with-mafft">Configure JABAWS to Work with Mafft</a></li>
 222 <li class="toctree-l3"><a class="reference internal" href="advanced.html#limiting-the-size-of-the-job-accepted-by-jabaws">Limiting the size of the job accepted by JABAWS</a></li>
 223 <li class="toctree-l3"><a class="reference internal" href="advanced.html#pre-compiled-binaries">Pre-compiled binaries</a></li>
 224 <li class="toctree-l3"><a class="reference internal" href="advanced.html#recompiling-binaries-for-your-system">Recompiling binaries for your system</a></li>
 225 <li class="toctree-l3"><a class="reference internal" href="advanced.html#obtaining-or-reusing-binaries">Obtaining or reusing binaries</a></li>
 226 </ul>
 227 </li>
 228 <li class="toctree-l2"><a class="reference internal" href="advanced.html#load-balancing">Load balancing</a></li>
 229 <li class="toctree-l2"><a class="reference internal" href="advanced.html#testing-the-jabaws-server">Testing the JABAWS Server</a></li>
 230 <li class="toctree-l2"><a class="reference internal" href="advanced.html#jabaws-internal-logging">JABAWS internal logging</a><ul>
 231 <li class="toctree-l3"><a class="reference internal" href="advanced.html#jabaws-requests-logging">JABAWS requests logging</a></li>
 232 </ul>
 233 </li>
 234 <li class="toctree-l2"><a class="reference internal" href="advanced.html#jabaws-and-google-analytics">JABAWS and Google Analytics</a></li>
 235 <li class="toctree-l2"><a class="reference internal" href="advanced.html#jabaws-war-file-content">JABAWS War File Content</a></li>
 236 </ul>
 237 </li>
 238 <li class="toctree-l1"><a class="reference internal" href="develop.html">For Developers</a><ul>
 239 <li class="toctree-l2"><a class="reference internal" href="develop.html#source-code">Source Code</a></li>
 240 <li class="toctree-l2"><a class="reference internal" href="develop.html#the-api">The API</a></li>
 241 <li class="toctree-l2"><a class="reference internal" href="develop.html#structure-of-the-project">Structure of the project</a></li>
 242 <li class="toctree-l2"><a class="reference internal" href="develop.html#the-code-structure">The code structure</a></li>
 243 <li class="toctree-l2"><a class="reference internal" href="develop.html#unit-testing">Unit Testing</a></li>
 244 <li class="toctree-l2"><a class="reference internal" href="develop.html#accessing-jabaws-from-your-program">Accessing JABAWS from your program</a><ul>
 245 <li class="toctree-l3"><a class="reference internal" href="develop.html#web-services-functions-overview">Web services functions overview</a></li>
 246 <li class="toctree-l3"><a class="reference internal" href="develop.html#structure-of-the-template-command-line-client">Structure of the template command line client</a></li>
 247 <li class="toctree-l3"><a class="reference internal" href="develop.html#connecting-to-jabaws">Connecting to JABAWS</a></li>
 248 <li class="toctree-l3"><a class="reference internal" href="develop.html#aligning-sequences">Aligning Sequences</a></li>
 249 <li class="toctree-l3"><a class="reference internal" href="develop.html#checking-the-status-of-the-calculation">Checking the status of the calculation</a></li>
 250 <li class="toctree-l3"><a class="reference internal" href="develop.html#aligning-with-presets">Aligning with presets</a></li>
 251 <li class="toctree-l3"><a class="reference internal" href="develop.html#aligning-with-custom-parameters">Aligning with custom parameters</a></li>
 252 <li class="toctree-l3"><a class="reference internal" href="develop.html#writing-alignments-to-a-file">Writing alignments to a file</a></li>
 253 <li class="toctree-l3"><a class="reference internal" href="develop.html#a-complete-client-example">A complete client example</a></li>
 254 </ul>
 255 </li>
 256 <li class="toctree-l2"><a class="reference internal" href="develop.html#adding-new-web-services">Adding new web-services</a><ul>
 257 <li class="toctree-l3"><a class="reference internal" href="develop.html#brief-guide">Brief Guide</a></li>
 258 <li class="toctree-l3"><a class="reference internal" href="develop.html#building-web-services-artifacts">Building web services artifacts</a></li>
 259 <li class="toctree-l3"><a class="reference internal" href="develop.html#preparing-distributives">Preparing Distributives</a></li>
 260 </ul>
 261 </li>
 262 </ul>
 263 </li>
 264 <li class="toctree-l1"><a class="reference internal" href="stats.html">Usage Statistics</a><ul>
 265 <li class="toctree-l2"><a class="reference internal" href="stats.html#detailed-view">Detailed View</a></li>
 266 <li class="toctree-l2"><a class="reference internal" href="stats.html#job-list">Job List</a></li>
 267 <li class="toctree-l2"><a class="reference internal" href="stats.html#job-directory-contents">Job Directory Contents</a></li>
 268 <li class="toctree-l2"><a class="reference internal" href="stats.html#configuring-jabaws-execution-statistics">Configuring JABAWS execution statistics</a></li>
 269 <li class="toctree-l2"><a class="reference internal" href="stats.html#configuring-a-privileged-access-for-tomcat-web-application-server">Configuring a privileged access for Tomcat web application server</a></li>
 270 </ul>
 271 </li>
 272 <li class="toctree-l1"><a class="reference internal" href="citations.html">Citations</a></li>
 273 <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
 274 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-2-released-xx-april-2017">Version 2.2 (Released XX April 2017)</a></li>
 275 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-1-released-1st-oct-2013">Version 2.1 (Released 1st Oct 2013)</a></li>
 276 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-0-1-released-2nd-jul-2013">Version 2.0.1 (Released 2nd Jul 2013)</a></li>
 277 <li class="toctree-l2"><a class="reference internal" href="changelog.html#version-2-released-16th-dec-2011">Version 2 (Released 16th Dec 2011)</a></li>
 278 </ul>
 279 </li>
 280 </ul>
 281 </div>
 282 <hr class="docutils" />
 283 <div class="admonition note">
 284 <p class="first admonition-title">Note</p>
 285 <p class="last">This is an open source project. If you want to contribute or report an issue have a look at our  <a class="reference external" href="https://source.jalview.org/crucible/changelog/jabaws">Git-tracker</a>.</p>
 286 </div>
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