2.3 updates

[jalview.git] / help / html / menus / wsmenu.html

diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index e2a9a4d..7584ca1 100755 (executable)
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -8,7 +8,12 @@
   on compute facilities at the University of Dundee. You need a continuous network \r
   connection in order to use these services through Jalview. </em> </p>\r
 <ul>\r
-  <li><strong>Alignment </strong> \r
+  <li><strong>Fetch DB References</strong><br>\r
+    This will use the service WSDBFetch, provided by the EBI, to retrieve all \r
+    database references and PDB ids associated with the selected sequences in \r
+    the alignment if the sequences have valid Uniprot names or accession ids. \r
+  </li>\r
+  <li><strong>Alignment</strong> \r
     <ul>\r
       <li><strong>ClustalW Multiple Sequence Alignment</strong><br>\r
         <em> Submits all, or just the currently selected sequences for alignment \r
@@ -17,8 +22,11 @@
         <em> Submits the alignment or currently selected region for re-alignment \r
         with clustal W. Use this if you have added some new sequences to an existing \r
         alignment.</em></li>\r
+      <li><strong>MAFFT Multiple Sequence Alignment</strong><br>\r
+        <em>Submits all, or just the currently selected region for alignment with \r
+        MAFFT. </em> </li>\r
       <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>\r
-        <em> Submits all, or jut the currently selected sequences for alignment \r
+        <em> Submits all, or just the currently selected sequences for alignment \r
         using Muscle. Do not use this if you are working with nucleic acid sequences.</em></li>\r
     </ul>\r
   </li>\r
@@ -36,8 +44,8 @@
         detection and prediction. </em></li>\r
       <li><em>If a set of sequences are selected, and they appear to be aligned, \r
         then the alignment will be used for a Jnet prediction on the <strong>first</strong> \r
-        sequence selected in the set (that is, the one that was first clicked \r
-        on). </em> </li>\r
+        sequence in the set (that is, the one that appears first in the alignment \r
+        window). </em> </li>\r
     </ul>\r
   </li>\r
 </ul>\r