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- <img src="images/align.gif" width="200" height="80" align="baseline"> Jalview \r
- Documentation </h1>\r
-<p align="center">Your guide to Jalview</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<head><title>Jalview Documentation</title></head>
+
+<body>
+<IMG src="Jalview_Logo.png">
+<p><strong>Welcome to Jalview's built in documentation.</strong></p>
+<p>Here are some good places to start:</p><ul>
+<li><a href="whatsNew.html">What's New</a> summarises the new features in this release of Jalview.</li>
+<li>Learn how to <a href="editing/index.html">edit alignments</a> with Jalview.</li>
+<li><a href="features/seqfeatures.html">Import and display sequence features on your alignment</a></li>
+<li>Use <a href="features/viewingpdbs.html">Jmol to view and superpose 3D structures</a> associated with sequences in the alignment</li>
+</ul>
+ <p>
+ For more information, you might also want to take a look at the
+ documentation section of the Jalview website (<a
+ href="http://www-test.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
+ </p>
+ <p>
+ If you are using the Jalview Desktop application and are looking for
+ something specific, then try the search box (next to the print icon).
+ If you're already viewing this in your web browser, then google the
+ online version of these pages. If you don't find what you are looking
+ for, or want to report a bug or make a feature request, then get in
+ contact over at <a href="http://www.jalview.org/community">http://www.jalview.org/community</a>
+ </p>
+
+ <p><strong>Citing Jalview</strong><br/>If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: </p>
+<p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
+ "Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"<br>
+ <em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033</p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff