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+<li><a href="jalviewLiteJs.html">Javascript API</a></li>
+<li><a href="formComplete.html">in-page API demo</a></li>
+<li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
+<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
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<p>
<strong>Quick Links:<ul><li>Download the applet jar file from <a
href="jalviewApplet.jar">here</a>
</font></li>
<li> Use Jalview for input to a HTML form. For an example of how to
code this using Javascript, click <a href="formComplete.html">here</a>.
- <br>\r
- </li>\r
+ <br>
+ </li>
<li>Embed Jalview into the web page, without the "Start Jalview"
button by setting the embed parameter to true;<br>
<param name="embedded"
<font size="2"><param name="PDBFile3" value="Third.pdb
D=SeqX B=SeqY C=SeqZ"> </font> <br>
</li>
- <li>Note parameter "PDBSeq" is no longer required.<br>\r
+ <li>Note parameter "PDBSeq" is no longer required.<br>
</li>
<li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li>
<p> </p>
<td>true of false (default is false)</td>
<td>When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (<em>since 2.7</em>)</td>
</tr>
- <tr><td>normaliseLogo</td>
+ <tr><td>normaliseSequenceLogo</td>
<td>true of false (default is false)</td>
<td>When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (<em>since 2.8</em>)</td>
</tr>
<td>Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format</td>
</tr>
</table>
- <p align="center"> </p>
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+<div id="copyright"><p>Copyright all rights reserved 2012</p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
+</p>
+</div>
+</div>
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git://source.jalview.org / jalview.git / blobdiff