2.5 updates...

diff --git a/help/html/releases.html b/help/html/releases.html
index fcb9534..e7ab682 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -30,7 +30,9 @@
                        <li>Linked viewing of nucleic acid sequences and structures</li>
                        <li>Automatic Scrolling option in View menu to display the
                        currently highlighted region of an alignment.</li>
-                       <li>Optionally scale multi-character column labels to fit within each column of annotation row<!-- todo for applet --></li>
+                       <li>Order an alignment in order of average feature score or
+                       total feature count</li>
+                       <li>Shading features by score or associated description</li>
                        <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
                </ul>
                <em>Vamsas Capabilities</em>
@@ -54,29 +56,36 @@
                        references in sequence ID tooltip from View menu in application.</li>
        <!--                    <li>New hidden columns and rows and representatives capabilities
                        in annotations file (in progress - not yet fully implemented)</li> -->
-                       <li>Order an alignment in order of average feature score or
-                       total feature count</li>
-                       <li>Shading features by score or associated description</li>
-                       <li>Group-associated automatic and user-defined alignment
-                       annotation</li>
+                       <li>Group-associated consensus, sequence logos and conservation plots</li>
                        <li>Symbol distributions for each column can be exported and
                        visualized as sequence logos</li>
+                       <li>Optionally scale multi-character column labels to fit within each column of annotation row<!-- todo for applet --></li>
                        <li>Optional automatic sort of associated alignment view when a
                        new tree is opened.</li>
                        <li>Jalview Java Console</li>
                        <li>New preference items for sequence ID tooltip and consensus annotation</li>
+                       <li>Client to submit sequences and IDs to <a href="webServices/index.html#envision2">Envision2</a> Workflows</li>
                </ul>
                <em>Applet</em>
                <ul>
                        <li>Middle button resizes annotation row height</li>
-                       <li>parameter to enable automatic sort of associated alignment view when a
-                       new tree is opened.</li>
-               <li>Non-positional features displayed in sequence ID tooltip</li>
+                       <li>New Parameters
+                       <ul>
+                        <li>sortByTree (true/false) - automatically sort the associated alignment view by the tree when a new tree is opened.</li>
+                        <li>showTreeBootstraps (true/false) - show or hide branch bootstraps (default is to show them if available)</li>
+                        <li>showTreeDistances (true/false) - show or hide branch lengths (default is to show them if available)</li>
+                        <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated nodes should be highlighted in the tree view</li>
+                        <li>heightScale and widthScale (1.0 or more) - increase the height or width of a cell in the alignment grid relative to the current font size.</li>
+                       </ul>
+                       </li>
+                       <li>Non-positional features displayed in sequence ID tooltip</li>
+               <li></li>
                </ul>
                <em>Other</em>
                <ul>
                        <li>Features format: graduated colour definitions and
                        specification of feature scores</li>
+                       <li>Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES)</li>
                        <li>XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.</li>
                </td>
                <td>
@@ -93,6 +102,7 @@
                        ID and sequence string and query strings do not have to be in upper
                        case to match case-insensitively.</li>
                        <li>AMSA files only contain first column of multi-character column annotation labels</li>
+                       <li>Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)</li>
                        <li>PDB files without embedded PDB IDs given a friendly name</li>
                        <li>Applet:
                        <ul>