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-<head><title>Home Page</title></head>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+-->
+<head><title>Jalview Documentation</title></head>
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+<IMG src="align.jpg"><font size="4">
<br><br>
<strong>Jalview Documentation</strong></font>
<br><br>
-Jalview (2004) is a fast Java multiple alignment editor and analysis tool. It
+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>).
+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 bioinformatics paper: </p>
-<p>Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview
- Java Alignment Editor", Bioinformatics, 20, 426-7.</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
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git://source.jalview.org / jalview.git / blobdiff