merge from develop

diff --cc examples/appletParameters.html
index d6c4edd,c880a84..a0f25d4
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--- 2/examples/appletParameters.html
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@@@ -456,4 -599,30 +456,4 @@@ the applet can be interacted with <em>v
              </pre>(All the usual Jalview File formats are valid, however each 
              new line in an alignment file must be entered as a parameter)</li>
          </ul>
- <!-- content end -->
 -        
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+ <!-- content end -->
 -
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 -</div> <!-- end content div -->
 -
 -</div> <!-- content -->
 -</div> <!-- pagewrap -->
 -<div id ="footer">
 -<div id="innerFooter">
 -<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></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 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 -</p>
 -</div>
 -</div>
 -</div>
 -</body>
 -</html>