updated release notes for Jalview Version 2.8

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                <div align="center"><em><strong>Issues Resolved</strong></em></div>
                </td>
        </tr>
+<tr>
+<td><div align="center"><strong><a name="Jalview2.8">2.8</a></strong><br/> <em>08/11/2012</em></div></td>
+<td><em>Application</em>
+<li>Support for JABAWS 2.0 Services (AACon alignment conservation, protein disorder and Clustal Omega) <!--[<a href='http://issues.jalview.org/browse/JAL-976'>JAL-976</a>] -         Enhance Jalview desktop to support to JABAWS v2.0 services -->
+<!--[<a href='http://issues.jalview.org/browse/JAL-974'>JAL-974</a>]--><!--[<a href='http://issues.jalview.org/browse/JAL-975'>JAL-975</a>]-->
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1060'>JAL-1060</a>] -        -->JABAWS server status indicator in Web Services preferences
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-842'>JAL-842</a>] -         -->VARNA (http://varna.lri.fr) viewer for RNA structures in Jalview alignment window
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1133'>JAL-1133</a>] -         -->Updated jalview build and deploy framework for OSX mountain lion, windows 7, and 8
+</li>
+<li>Nucleotide substitution matrix for PCA that supports RNA and ambiguity codes <!--[<a href='http://issues.jalview.org/browse/JAL-1027'>JAL-1027</a>] -->
+</li>
+
+<li>Improved sequence database retrieval GUI</li><li>Support fetching and database reference look up against multiple DAS sources<!--[<a href='http://issues.jalview.org/browse/JAL-1061'>JAL-1061</a>], [<a href='http://issues.jalview.org/browse/JAL-1075'>JAL-1075</a>] -         GUI elements to select one or several DAS sources to query for sequences or database references-->
+</li>
+<li>Jalview project improvements<ul><li><!--[<a href='http://issues.jalview.org/browse/JAL-1109'>JAL-1109</a>] -->Store and retrieve the &#39;belowAlignment&#39; flag for annotation</li><li><!--[<a href='http://issues.jalview.org/browse/JAL-1110'>JAL-1110</a>]-->calcId attribute to group annotation rows on the alignment</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1136'>JAL-1136</a>] -         -->Store AACon calculation settings for a view in Jalview project
+</li>
+
+</ul>
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1160'>JAL-1160</a>] -         -->horizontal scrolling gesture support
+</li>
+<li>Visual progress indicator when PCA calculation is running<!--[<a href='http://issues.jalview.org/browse/JAL-1120'>JAL-1120</a>] -         -->
+</li>
+<li>Simpler JABA web services menus<!--[<a href='http://issues.jalview.org/browse/JAL-1137'>JAL-1137</a>] -         -->
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1165'>JAL-1165</a>] -         -->visual indication that web service results are still being retrieved from server 
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1183'>JAL-1183</a>] -         -->Serialise the dialogs that are shown when jalview starts up for first time
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1188'>JAL-1188</a>] -         -->Jalview user agent string for interacting with HTTP services
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-972'>JAL-972</a>] -         -->DAS 1.6 and DAS 2.0 source support using new JDAS client library
+</li>
+</ul>
+<em>Applet</em>
+<ul><li><!--[<a href='http://issues.jalview.org/browse/JAL-963'>JAL-963</a>] -         -->RNA alignment and secondary structure annotation visualization applet example 
+</li>
+</ul>
+<em>General</em>
+<ul><li><!--[<a href='http://issues.jalview.org/browse/JAL-958'>JAL-958</a>] -         -->Normalise option for consensus sequence logo
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1121'>JAL-1121</a>] -         -->Reset button in PCA window to return dimensions to defaults
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1125'>JAL-1125</a>] -         -->Allow seqspace or Jalview variant of alignment PCA calculation
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1013'>JAL-1013</a>] -->PCA with either nucleic acid and protein substitution matrices
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1157'>JAL-1157</a>] -         -->Allow windows containing HTML reports to be exported in HTML
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-970'>JAL-970</a>] -         -->Interactive display and editing of RNA secondary structure contacts
+</li>
+<li>RNA Helix Alignment Colouring</li>
+<li>RNA base pair logo consensus</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-878'>JAL-878</a>] -         -->Parse sequence associated secondary structure information in Stockholm files
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1015'>JAL-1015</a>] -         -->HTML Export database accessions and annotation information presented in tooltip for sequences
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1052'>JAL-1052</a>] -        -->Import secondary structure from LOCARNA clustalw style RNA alignment files
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1065'>JAL-1065</a>] - [<a href='http://issues.jalview.org/browse/JAL-1078'>JAL-1078</a>]-->import and visualise T-COFFEE quality scores for an alignment
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1066'>JAL-1066</a>] -        -->&#39;colour by annotation&#39; per sequence option to shade each sequence according to its associated alignment annotation
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1130'>JAL-1130</a>] -         -->New Jalview Logo
+</li>
+</ul>
+<em>Documentation and Development</em>
+<ul><li><!--[<a href='http://issues.jalview.org/browse/JAL-1167'>JAL-1167</a>] -         -->documentation for score matrices used in Jalview
+</li>
+<li>New Website!
+</li>
+</ul>
+</td><td>
+<em>Application</em>
+<ul><li>PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch REST service<!--<a href='http://issues.jalview.org/browse/JAL-636'>JAL-636</a>-->
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-368'>JAL-368</a>] -         --><!--[<a href='http://issues.jalview.org/browse/JAL-153'>JAL-153</a>] -        -->Stop windows being moved outside desktop on OSX
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-758'>JAL-758</a>] -         -->Filetype associations not installed for webstart launch
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-849'>JAL-849</a>] -         -->Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-979'>JAL-979</a>] -         -->revise SHMR RSBS definition to ensure alignment is uploaded via ali_file parameter
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-980'>JAL-980</a>] -         -->Jalview 2.7 is incompatible with Jmol-12.2.2
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-983'>JAL-983</a>] -         -->View all structures superposed fails with exception
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-994'>JAL-994</a>] -         -->Jnet job queues forever if a very short sequence is submitted for prediction
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1004'>JAL-1004</a>] -         -->Cut and paste menu not opened when mouse clicked on desktop window
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1010'>JAL-1010</a>] -         -->Putting fractional value into integer text box in alignment parameter dialog causes jalview to hang
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1022'>JAL-1022</a>] -         -->Structure view highlighting doesn&#39;t work on windows 7
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1023'>JAL-1023</a>] -         -->View all structures fails with exception shown in structure view
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1025'>JAL-1025</a>] -         -->Characters in filename associated with PDBEntry not escaped in a platform independent way 
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1026'>JAL-1026</a>] -         -->Jalview desktop fails to launch with exception when using proxy
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1031'>JAL-1031</a>] -         -->Tree calculation reports &#39;you must have 2 or more sequences selected&#39; when selection is empty
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1040'>JAL-1040</a>] -         -->Jalview desktop fails to launch with jar signature failure when java web start temporary file caching is disabled
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1062'>JAL-1062</a>] -         -->DAS Sequence retrieval with range qualification results in sequence xref which includes range qualification
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1087'>JAL-1087</a>] -         -->Errors during processing of command line arguments cause progress bar (JAL-898) to be removed
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1097'>JAL-1097</a>] -         -->Replace comma for semi-colon option not disabled for DAS sources in sequence fetcher
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1111'>JAL-1111</a>] -         -->Cannot close news reader when JABAWS server warning dialog is shown
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1127'>JAL-1127</a>] -         -->Option widgets not updated to reflect user settings
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1131'>JAL-1131</a>] -         -->Edited sequence not submitted to web service
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1134'>JAL-1134</a>] -         -->Jalview 2.7 Webstart does not launch on mountain lion
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1135'>JAL-1135</a>] -         -->InstallAnywhere installer doesn&#39;t unpack and run on OSX Mountain Lion
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1144'>JAL-1144</a>] -         -->Annotation panel not given a scroll bar when sequences with alignment annotation are pasted into the alignment
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1148'>JAL-1148</a>] -         -->Sequence associated annotation rows not associated when loaded from jalview project
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] -         -->Browser launch fails with NPE on java 1.7
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1171'>JAL-1171</a>] -         -->JABAWS alignment marked as finished when job was cancelled or job failed due to invalid input
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1185'>JAL-1185</a>] -         -->NPE with v2.7 example when clicking on Tree associated with all views
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1145'>JAL-1145</a>] -         -->Exceptions when copy/paste sequences with grouped annotation rows to new window
+</li>
+</ul>
+
+
+<em>Applet</em>
+<ul><li><!--[<a href='http://issues.jalview.org/browse/JAL-962'>JAL-962</a>] -         -->Sequence features are momentarily displayed before they are hidden using hidefeaturegroups applet parameter
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-965'>JAL-965</a>] -         -->loading features via javascript API automatically enables feature display
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1170'>JAL-1170</a>] -         -->scrollToColumnIn javascript API method doesn&#39;t work
+</li>
+</ul>
+<em>General</em>
+<ul><li><!--[<a href='http://issues.jalview.org/browse/JAL-1007'>JAL-1007</a>] -         -->Redundancy removal fails for rna alignment
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1032'>JAL-1032</a>] -         -->PCA calculation fails when sequence has been selected and then deselected
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1033'>JAL-1033</a>] -         -->PCA window shows grey box when first opened on OSX
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1086'>JAL-1086</a>] -        -->Letters coloured pink in sequence logo when alignment coloured with clustalx
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1099'>JAL-1099</a>] -         -->Choosing fonts without letter symbols defined causes exceptions and redraw errors
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1123'>JAL-1123</a>] -         -->Initial PCA plot view is not same as manually reconfigured view
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1153'>JAL-1153</a>] -         -->Grouped annotation graph label has incorrect line colour
+</li>
+<li><!--[<a href='http://issues.jalview.org/browse/JAL-1155'>JAL-1155</a>] -         -->Grouped annotation graph label display is corrupted for lots of labels
+</li>
+</ul>
+
+</tr>
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