-<p><strong>What's new ?</strong></p>
-<p><strong>Highlights in Jalview Version 2.4</strong></p>
-<ul>
- DNA and protein product highlighting<br>
- URL links generated with regular expressions<br>
- URL links for sequence database cross references<br>
- New sequence fetcher dialog and DAS Sequence Fetching<br>
- JPred Service upgraded to Jpred3<br>
- Memory monitor<br>
- PFAM full alignment retrieval<br>
- Generalised sequence database reference validation<br>
- DNA Protein Product sequence db traversal (Experimental)<br>
- VAMSAS Interoperation Client (Experimental)<br>
- export annotation rows as CSV for spreadsheet import<br>
- New application command line args and optional Groovy suport<br>
- New Applet API methods and parameters<br>
-</ul>
-<p><strong>Issues Resolved (a select list)</strong></p>
-<ul>
- Aligned cDNA translation to aligned peptide works correctly<br>
- selected region output includes visible annotations (for
- certain formats)<br>
- edit label/displaychar contains existing label/char for
- editing<br>
- Newick tree support improved for clustalW trees and preserving NHX style comments<br>
- Pathological filechooser bug avoided by not allowing
- filenames containing a ':'<br>
- Fixed exception when parsing GFF files containing global
- sequence features<br>
- Reference counting for alignment datasets<br>
- better reporting of non-fatal warnings and error messages to user when file
- parsing fails.<br>
- Save works when Jalview project is default format<br>
- Histidine should be midblue (not pink!) in Zappo<br>
- Undo recovers dataset sequence metadata when sequence
- regions are cut<br>
- PDB files without pdb ID HEADER lines (like those
- generated by MODELLER) are read in properly<br>
- Stockholm annotation parsing fixed and improved (PFAM records)<br>
- Re-instated Full AMSA support and .amsa file association (MyHits)<br>
- annotation consisting of sequence associated scores can be
- read and written correctly to annotation file<br>
- Fixed display of hidden sequence markers and non-italic font
- for representatives in Applet<br>
- Applet Menus are always embedded in applet window on Macs.</br>
- Newly shown features appear at top of stack (in Applet)</br>
- Secondary structure lines are drawn starting from first
- column of alignment<br>
- Uniprot XML import updated for new schema release in July 2008<br>
- Sequence feature to sequence ID match for Features file is case-insensitive<br>
- Sequence features read from Features file appended to all sequences with matching IDs<br>
- PDB structure coloured correctly for associated views containing a sub-sequence<br>
- Display name and local features preserved in results retrieved from web service<br>
- Visual delay indication for sequence retrieval and sequence fetcher initialisation<br>
- Updated Application to use DAS 1.53e version of dasobert DAS client
-</ul>
+ <p>
+ <strong>What's new ?</strong>
+ </p>
+ <p>Jalview 2.8 includes a brand new logo, which you'll see in file
+ browsers, splash screens, and also on the new look Jalview site.</p>
+ <p>
+ In addition to our new look, Jalview 2.8 includes a number of new
+ features.. some of which have been in development since July 2010. The
+ highlights are below, and - as usual, for a comprehensive list, take a
+ look at the <a href="releases.html#Jalview2.8">Jalview 2.8 Release
+ Notes</a>.
+ </p>
+ <p>
+ <strong>Highlights in Jalview Version 2.8</strong>
+ </p>
+ <ul>
+ <li>Improved JABA client and new JABAWS 2.0 Services
+ <ul>
+ <li>AACon alignment conservation</li>
+ <li>Protein disorder - DisEMBL, RONN, GlobPlot and IUPred</li>
+ <li>Clustal Omega - huge protein alignments</li>
+ </ul>
+ </li>
+ <li><strong>Support for RNA</strong>
+ <ul>
+ <li>Import sequence and alignment associated WUSS or VIENNA
+ secondary structure notation from stockholm and clustalW files or
+ as jalview annotation.</li>
+ <li>Interactive editing of RNA secondary structure annotation</li>
+ <li>Colour scheme for purine/pyrimidine and to highlight RNA
+ helices</li>
+ <li>RNA canonical base pair consensus score and sequence logo</li>
+ <li>Embedded <a href="http://varna.lri.fr/">VARNA</a> RNA
+ secondary structure viewer in the Desktop
+ </li>
+ </ul> See <a href="na/index.html">Nucleic Acid Support</a> for full
+ details.</li>
+ <li>Parse and display T-COFFEE alignment quality scores</li>
+ <li>Shade individual sequence positions according to alignment
+ annotation scores</li>
+ <li>Enhanced PCA viewer: more export options, and switch between
+ different PCA modes and residue score models</li>
+ <li>New Jalview Desktop database fetcher GUI</li>
+ <li>Support for DAS 1.6 and DAS 2.0 sources</li>
+ <li>Export sequence database annotation as HTML report</li>
+ <li>Normalised Sequence Logo Display</li>
+ </ul>
+ <p>
+ <strong>Issues Resolved (a select list - see the <a
+ href="releases.html#Jalview2.8">release history</a> for full details)
+ </strong>
+ </p>
+ <p>
+ <strong>Issues in the Jalview Desktop</strong>
+ <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-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-1022'>JAL-1022</a>] - -->Structure
+ view highlighting doesn't work on windows 7
+ </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 'you must have 2 or more sequences
+ selected' when selection is empty
+ </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-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-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 and InstallAnywhere installer doesn't unpack and run
+ on OSX Mountain Lion
+ <ul>
+ <li>The workaround for webstart is to go into the Security
+ panel (gatekeeper symbol) under System settings, and select the
+ 'allow any code to run' setting.</li>
+ </ul>
+ </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-1145'>JAL-1145</a>] - -->Exceptions
+ when copy/paste sequences with grouped annotation rows to new window
+ </li>
+ <li>
+ <!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] - -->Browser
+ launch fails with NPE on java 1.7
+ </li>
+
+ </ul>