3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>Jalview Documentation</title></head>
22 <IMG src="Jalview_Logo.png">
23 <p><strong>Welcome to Jalview's built in documentation.</strong></p>
24 <p>If you don't know what Jalview is, then in addition to the pages here, we also suggest you take a look at www.jalview.org.</p>
25 <p>Here are some good places to start:</p><ul>
26 <li><a href="whatsNew.html">What's New"</a> summarises the new features in this release of Jalview.</li>
27 <li>Learn how to <a href="editing/index.html">edit alignments</a> with Jalview.</li>
28 <li><a href="features/seqfeatures.html">Import and display sequence features on your alignment</a></li>
29 <li>Use <a href="features/viewingpdbs.html">Jmol to view and superpose 3D structures</a> associated with sequences in the alignment</li>
31 <p>If you are using the Jalview Desktop application and are looking
32 for something specific, then this help system also includes a search
33 box. If you're already viewing this in your web browser, then google
34 the online version of these pages. If you don't find what you are
35 looking for, or want to report a bug or make a feature request, then
36 get in contact over at <a href="http://www.jalview.org/community">http://www.jalview.org/community</a></p>
38 <p><strong>Citing Jalview</strong><br/>If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: </p>
39 <p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
40 "Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"<br>
41 <em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033</p>