X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2FhelpTOC.xml;h=5dec60151db23f516f7905d85d17f448f1f92ae9;hb=ae3b7664d0d98f376b1f636edc34aaff6b8a914a;hp=92655994947fe7777bcc14f12143abbdead69324;hpb=20bddfcf8ef1a53bce455b7599f8066b8ccba0d4;p=jalview.git

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 9265599..5dec601 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,9 +3,11 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="false">
-        	<tocitem text="MAFFT Alignment" target="mafft"/>
         	<tocitem text="DAS Feature Fetching" target="das.settings"/>
-        	<tocitem text="Hide Regions" target="hiddenRegions"/> 	         
+        	<tocitem text="Hide Regions" target="hiddenRegions"/>
+              	<tocitem text="Tree/PCA Input Data" target="recoverInputdata"/>
+                <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
+        	<tocitem text="MAFFT Alignment" target="mafft"/>
         </tocitem>
         <tocitem text="Release History" target="release"/>
         <tocitem text="Editing Alignments" target ="edit"/>	
@@ -19,13 +21,15 @@
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
           <tocitem text="User Defined Sequence Features" target="search"/>
-          <tocitem text="DAS Features Settings" target="das.settings"/>
+          <tocitem text="DAS Features Settings" target="das.viewing"/>
         </tocitem>
 	<tocitem text="Web Services" target="webservice" expand="false">
+          <tocitem text="Sequence Alignment" target="msaservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
                 <tocitem text="Muscle Alignment" target="muscle"/>
                 <tocitem text="MAFFT Alignment" target="mafft"/>
-          	<tocitem text="JNet Prediction" target="jnet"/>
+            </tocitem>
+          <tocitem text="Secondary Structure Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="ClustalX" target="colours.clustal"/>