JAL-1632 removed ‘tree’ option and changed dialog layout

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

diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index ee44c91..b71bc1a 100755 (executable)
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -55,13 +55,12 @@
     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 +68,22 @@
       <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 +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
-            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>