X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2Fwsmenu.html;h=b8b357ed860bf07789eb8a584a6abbd8b7819977;hb=a510e9b4726214441e4fdac8a1d6752263c4c73d;hp=312fece11ab154683643e579ef194eed67759dbb;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index 312fece..b8b357e 100755
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -1,7 +1,7 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -29,14 +29,13 @@
       dynamic, and may contain user-defined web service entries in
       addition to any of the following ones:</em>
   <ul>
-    <li><strong>Fetch DB References</strong><br> <em>This
-        submenu contains options for accessing any of the database
-        services that Jalview is aware of (e.g. DAS sequence servers and
-        the WSDBFetch service provided by the EBI) to verify sequence
-        start/end positions and retrieve all database cross references
-        and PDB ids associated with all or just the selected sequences
-        in the alignment.
-        <ul>
+    <li><strong>Fetch DB References</strong><br> <em>This submenu
+				contains options for accessing any of the database services that
+				Jalview is aware of (e.g services provided by the EBI) to verify
+				sequence start/end positions and retrieve all database cross
+				references and PDB ids associated with all or just the selected
+				sequences in the alignment.
+				<ul>
           <li>'Retrieve full Sequence' - when checked, Jalview will
             retrieve the full sequence for any accessions associated
             with sequences in the alignment. <br> <strong>Note:
@@ -45,7 +44,7 @@
               in Jalview 2.8.1</strong>
           </li>
           <li>'Standard Databases' will check sequences against the
-            EBI databases plus any active DAS sequence sources<</li>
+            EBI databases</li>
         </ul> Other submenus allow you to pick a specific source to query -
         sources are listed alphabetically according to their nickname.
     </em></li>
@@ -55,13 +54,12 @@
     elsewhere. You need a continuous network connection in order to use
     these services through Jalview.</p>
   <ul>
-    <li><strong>Alignment</strong><br />
-    <em> Align the currently selected sequences or all sequences in
-        the alignment, or re-align unaligned sequences to the aligned
-        sequences. Entries in this menu provide access to the various
-        alignment programs supported by <a
-        href="../webServices/JABAWS.html"
-      >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
+    <li><strong>Alignment</strong><br /> <em> Align the
+        currently selected sequences or all sequences in the alignment,
+        or re-align unaligned sequences to the aligned sequences.
+        Entries in this menu provide access to the various alignment
+        programs supported by <a href="../webServices/JABAWS.html">JABAWS</a>.
+        See the <a href="../webServices/msaclient.html">Multiple
           Sequence Alignment webservice client</a> entry for more
         information.
     </em></li>
@@ -69,22 +67,22 @@
       <ul>
         <li><strong>JPred Secondary Structure Prediction</strong><br>
           <em>Secondary structure prediction by network consensus.
-            See the <a href="../webServices/jnet.html">Jpred3</a> client
+            See the <a href="../webServices/jnet.html">Jpred</a> client
             entry for more information. The behaviour of this
             calculation depends on the current selection:
             <ul>
               <li>If nothing is selected, and the displayed
-                sequences appear to be aligned, then a JNet prediction
+                sequences appear to be aligned, then a JPred prediction
                 will be run for the first sequence in the alignment,
                 using the current alignment. Otherwise the first
                 sequence will be submitted for prediction.</li>
               <li>If just one sequence (or a region on one
                 sequence) has been selected, it will be submitted to the
-                automatic JNet prediction server for homolog detection
+                automatic JPred prediction server for homolog detection
                 and prediction.</li>
               <li>If a set of sequences are selected, and they
                 appear to be aligned, then the alignment will be used
-                for a Jnet prediction on the <strong>first</strong>
+                for a JPred prediction on the <strong>first</strong>
                 sequence in the set (that is, the one that appears first
                 in the alignment window).
               </li>
@@ -96,8 +94,8 @@
         <li><strong>Multi-Harmony</strong><br> <em>Performs
             functional residue analysis on a protein family alignment
             with sub-families defined on it. See the <a
-            href="../webServices/shmr.html"
-          >Multi-Harmony service</a> entry for more information.
+            href="../webServices/shmr.html">Multi-Harmony
+              service</a> entry for more information.
         </em></li>
       </ul></li>
   </ul>
