sort by score

diff --git a/help/html/calculations/sorting.html b/help/html/calculations/sorting.html
index 47522ee..1c15890 100755 (executable)
--- a/help/html/calculations/sorting.html
+++ b/help/html/calculations/sorting.html
@@ -34,8 +34,13 @@ alignments by some measure of sequence identity.<br>
 If the current alignment has been generated by one of Jalview's
 alignment web services, the alignment ordering can be recovered by
 its corresponding entry in the Sort menu.
 If the current alignment has been generated by one of Jalview's
 alignment web services, the alignment ordering can be recovered by
 its corresponding entry in the Sort menu.

-</p><p>
+</p>

 </li>
 </li>

+<li><p><strong>Sort by Score</strong></p>
+<p>This menu appears if the alignment contains any <a href="../features/annotationsFormat.html">sequence associated
+alignment annotation</a> with associated score values. Each entry is the
+label for a distinct group of sequence associated annotation
+scores which can be used for sorting.</p>

 </ul>
 <p><strong>Reversing the Order</strong></p>
 <p>Selecting any item from the Sort menu will sort sequences in an
 </ul>
 <p><strong>Reversing the Order</strong></p>
 <p>Selecting any item from the Sort menu will sort sequences in an

diff --git a/help/html/menus/alwcalculate.html b/help/html/menus/alwcalculate.html
index 9d40868..6ee7ed8 100755 (executable)
--- a/help/html/menus/alwcalculate.html
+++ b/help/html/menus/alwcalculate.html
@@ -18,7 +18,8 @@
         identity to the consensus sequence. The most similar sequence is put at 
         the top. </em></li>
       <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have 
         identity to the consensus sequence. The most similar sequence is put at 
         the top. </em></li>
       <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will have 

-        some additional options if you have just done a multiple alignment calculation, 
+        some additional options if the alignment has any associated
+       score annotation, or you have just done a multiple alignment calculation

         or opened a tree viewer window.</em><br>
       </li>
     </ul>
         or opened a tree viewer window.</em><br>
       </li>
     </ul>