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Merge branch 'develop' into releases/Release_2_10_3_Branch
[jalview.git] / help / html / menus / wsmenu.html
diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index 753f4f6..b71bc1a 100755 (executable)
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -1,7 +1,7 @@
 <html>
 <!--
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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.
  * 
  * 
  * This file is part of Jalview.
  * 
@@ -55,13 +55,12 @@
     elsewhere. You need a continuous network connection in order to use
     these services through Jalview.</p>
   <ul>
     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>
           Sequence Alignment webservice client</a> entry for more
         information.
     </em></li>
@@ -69,22 +68,22 @@
       <ul>
         <li><strong>JPred Secondary Structure Prediction</strong><br>
           <em>Secondary structure prediction by network consensus.
       <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
             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
                 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
                 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>
                 sequence in the set (that is, the one that appears first
                 in the alignment window).
               </li>
@@ -96,8 +95,8 @@
         <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
         <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>
         </em></li>
       </ul></li>
   </ul>