3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
22 <head><title>Jalview Documentation</title></head>
25 <IMG src="Jalview_Logo.png">
26 <p><strong>Welcome to Jalview's built in documentation.</strong></p>
27 <p>Here are some good places to start:</p><ul>
28 <li><a href="whatsNew.html">What's New</a> summarises the new features in this release of Jalview.</li>
29 <li>Learn how to <a href="editing/index.html">edit alignments</a> with Jalview.</li>
30 <li><a href="features/seqfeatures.html">Import and display sequence features on your alignment</a></li>
31 <li>Use <a href="features/viewingpdbs.html">Jmol to view and superpose 3D structures</a> associated with sequences in the alignment</li>
34 For more information, you might also want to take a look at the
35 documentation section of the Jalview website (<a
36 href="http://www-test.jalview.org/about/documentation">http://www.jalview.org/about/documentation</a>).
39 If you are using the Jalview Desktop application and are looking for
40 something specific, then try the search box (next to the print icon).
41 If you're already viewing this in your web browser, then google the
42 online version of these pages. If you don't find what you are looking
43 for, or want to report a bug or make a feature request, then get in
44 contact over at <a href="http://www.jalview.org/community">http://www.jalview.org/community</a>
47 <p><strong>Citing Jalview</strong><br/>If you use Jalview in your work, please cite the Jalview 2 paper in Bioinformatics: </p>
48 <p>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M., Barton, G.J (2009), <br>
49 "Jalview version 2: A Multiple Sequence Alignment and Analysis Workbench,"<br>
50 <em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033</p>
51 <p><strong>The Jalview Authors</strong><br/>
52 The following people have contributed to Jalview's development:
55 <ul><li>Michele Clamp</li>
61 </li><li>Jalview 2<ul>
63 <li>Andrew Waterhouse</li>
64 <li>Mungo Carstairs</li>
65 <li>Tochukwu 'Charles' Ofoegbu</li>
66 <li>Jan Engelhardt</li>
69 <li>Natasha Sherstnev</li>
70 <li>Daniel Barton</li>
71 <li>David Roldan-Martinez</li>