-<html>\r
-<head><title>Home Page</title></head>\r
-\r
-<body>\r
-<IMG src="align.gif"><font size="4">\r
-<br><br>\r
-<strong>Jalview Documentation</strong></font>\r
-<br><br>\r
-JalView (1999) is a fast Java multiple alignment editor and analysis tool. It\r
-features many of the functions of <a href="http://www.compbio.dundee.ac.uk/Software/Amas/amas.html">AMAS</a>,\r
-for the analysis of sub-families and the prediction of functional sites, but is\r
-fully interactive.\r
-<p></p>\r
-<p> If you use JalView in your work, please cite the bioinformatics paper: </p>\r
-<p>Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview\r
- Java Alignment Editor", Bioinformatics, 20, 426-7.</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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>
+ <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