<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
+ * 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/>.
--->
-<head><title>Jalview Documentation</title></head>
+ * 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="align.jpg"><font size="4">
-<br><br>
-<strong>Jalview Documentation</strong></font>
-<br><br>
-Jalview (2009) is a fast Java multiple alignment editor and analysis tool. It
-features many of the functions of <a href="http://www.compbio.dundee.ac.uk/Software/Amas/amas.html">AMAS</a>,
-for the analysis of sub-families and the prediction of functional sites, but is
-fully interactive. (View the <a href="http://www.jalview.org">Jalview homepage</a> at www.jalview.org).
-<p></p>
-<p> 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
+ <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>
+ <p>
+ <strong>The Jalview Authors</strong><br /> The following people have
+ contributed to Jalview's development:
+ <ul>
+ <li>Jalview 1
+ <ul>
+ <li>Michele Clamp</li>
+ <li>James Cuff</li>
+ <li>Steve Searle</li>
+ <li>David Martin</li>
+ <li>Geoff Barton</li>
+ </ul>
+ </li>
+ <li>Jalview 2
+ <ul>
+ <li>Jim Procter</li>
+ <li>Andrew Waterhouse</li>
+ <li>Mungo Carstairs</li>
+ <li>Tochukwu 'Charles' Ofoegbu</li>
+ <li>Jan Engelhardt</li>
+ <li>Lauren Lui</li>
+ <li>Anne Menard</li>
+ <li>Natasha Sherstnev</li>
+ <li>Daniel Barton</li>
+ <li>David Roldan-Martinez</li>
+ <li>David Martin</li>
+ <li>Geoff Barton</li>
+ </ul>
+ </li>
+ </ul>
+ </p>
</body>
</html>
git://source.jalview.org / jalview.git / blobdiff