X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=d9a93040c174d09b9068e2413789c8cf1f9455ec;hb=11d7be472ca5ea89d69e5bb7882c0058b2c3c4b9;hp=f8b6d2948752077f3562d452744429ac8999d307;hpb=e50faa2d7e8c3d056955be397920c17bcf99bcf7;p=jalview.git

diff --git a/help/html/releases.html b/help/html/releases.html
index f8b6d29..d9a9304 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -62,25 +62,20 @@
             </ul>
           </li>
           <li>Jmol integration updated to Jmol v14.2.14</li>
-          <li>Import and export of Jalview alignment views as <a href="">BioJSON</a></li>
+          <li>Import and export of Jalview alignment views as <a
+            href="">BioJSON</a></li>
           <li>New alignment annotation file statements for
             reference sequences and marking hidden columns</li>
-          <li>Assign an alignment reference sequence to highlight
-            variation</li>
+          <li>Reference sequence based alignment shading to
+            highlight variation</li>
           <li>Select or hide columns according to alignment
             annotation</li>
-          <li>Find option for locating sequences by
-            description</li>
+          <li>Find option for locating sequences by description</li>
           <li>Conserved physicochemical properties shown in amino
             acid conservation row</li>
           <li>Alignments can be sorted by number of RNA helices</li>
-        </ul>
-        <em>Application</em>
+        </ul> <em>Application</em>
         <ul>
-          <li>Optional embedding of BioJSON data when exporting
-            alignment figures to HTML</li>
-          <li>New Export Settings dialog to control hidden region
-            export in flat file generation</li>
           <li>New cDNA/Protein analysis capabilities
             <ul>
               <li>Get Cross-References should open a Split Frame
@@ -93,58 +88,70 @@
           </li>
 
           <li>Use REST API to talk to Chimera</li>
-          <li>Selected regions in Chimera are highlighted in linked Jalview windows</li>
-
-          <li>Calculate UPGMA and NJ trees using sequence feature
-            similarity</li>
+          <li>Selected regions in Chimera are highlighted in linked
+            Jalview windows</li>
 
           <li>VARNA RNA viewer updated to v3.93</li>
-          <li>VARNA views are saved in Jalview
-            Projects</li>
-          <li>Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA</li>
-
-          <li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
-          <li>change "View protein structure" menu option to "3D Structure ..."</li>
+          <li>VARNA views are saved in Jalview Projects</li>
+          <li>Pseudoknots displayed as Jalview RNA annotation can
+            be shown in VARNA</li>
 
           <li>Make groups for selection uses marked columns as well
             as the active selected region</li>
 
-          <li>allow different similarity matrix calculations for
-            tree building and PCA</li>
+          <li>Calculate UPGMA and NJ trees using sequence feature
+            similarity</li>
+          <li>New Export options
+            <ul>
+              <li>New Export Settings dialog to control hidden
+                region export in flat file generation</li>
 
-          <li>Export alignment views for display with the <a
-            href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
-            
-          <li>Export scrollable SVG in HTML page</li>
+              <li>Export alignment views for display with the <a
+                href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
 
-          <li>Interactive free text and structured queries with the
-            PDBe Search API for PDB data retrieval</li>
-          <li>PDBe Search API based discovery and selection of PDB structures to
-            view for a sequence set</li>
+              <li>Export scrollable SVG in HTML page</li>
+              <li>Optional embedding of BioJSON data when exporting
+                alignment figures to HTML</li>
+          </li>
+          <li>3D structure retrieval and display
+            <ul>
+              <li>Free text and structured queries with
+                the PDBe Search API</li>
+              <li>PDBe Search API based discovery and selection of
+                PDB structures for a sequence set</li>
+            </ul>
+          </li>
 
           <li>JPred4 employed for protein secondary structure
             predictions</li>
           <li>Hide Insertions menu option to hide unaligned columns
             for one or a group of sequences</li>
-          <li>Automatically hide insertions in alignments imported from the JPred4 web server</li>
+          <li>Automatically hide insertions in alignments imported
+            from the JPred4 web server</li>
           <li>(Nearly) Native 'Quaqua' dialogs for browsing file
             system on OSX<br />LGPL libraries courtesy of <a
             href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
           </li>
+          <li>changed 'View nucleotide structure' submenu to 'View
+            VARNA 2D Structure'</li>
+          <li>change "View protein structure" menu option to "3D
+            Structure ..."</li>
+
         </ul> <em>Applet</em>
         <ul>
-          <li>New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)</li>
+          <li>New layout for applet example pages</li>
+          <li>New parameters to enable SplitFrame view (file2,enableSplitFrame,
+            scaleProteinAsCdna)</li>
           <li>New example demonstrating linked viewing of cDNA and
             Protein alignments</li>
-          <li>New layout for applet example pages</li>
-        </ul>
-        <em>Development and deployment</em>
+        </ul> <em>Development and deployment</em>
+        <ul>
         <li>Java 1.7 minimum requirement for Jalview 2.9</li>
         <li>Include installation type and git revision in build
           properties and console log output</li>
-        <li>Github project and web URL for storing BioJsMSA
-          Templates</li>
-        <li>Jalview's unit tests now managed with TestNG</li></td>
+        <li>Jalview Github organisation, and new github site for
+          storing BioJsMSA Templates</li>
+        <li>Jalview's unit tests now managed with TestNG</li></ul></td>
       <td>
         <!-- <em>General</em>
         <ul>