<head><title>Jalview Documentation</title></head>
<body>
-<IMG src="Jalview_Logo.png"><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>
+<IMG src="Jalview_Logo.png">
+<p><strong>Welcome to Jalview's built in documentation.</strong></p>
+<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>
+<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>If you are using the Jalview Desktop application and are looking
+ for something specific, then this help system also includes a search
+ box. 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
+ <em>Bioinformatics</em> <strong>25</strong> (9) 1189-1191 doi: 10.1093/bioinformatics/btp033</p>
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git://source.jalview.org / jalview.git / blobdiff