X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmenus%2FalignmentMenu.html;h=3a057a8567b9f4801af371898373e9147a790ad5;hb=54cbe6eeaf683e042246c657716514d80e561a9c;hp=00a2ec405971542b021a483760a965ebf40be132;hpb=80ac7d84002118186a11658f38abfa5c4fe3d8da;p=jalview.git

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index 00a2ec4..3a057a8 100755
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -314,9 +314,7 @@
             href="../features/featuresettings.html">Sequence
               Feature Settings...</a> </strong><br> <em>Opens the
               Sequence Feature Settings dialog box to control the colour
-              and display of sequence features on the alignment, and
-              configure and retrieve features from DAS annotation
-              servers.</em></li>
+              and display of sequence features on the alignment.</em></li>
         <li><strong>Sequence ID Tooltip</strong><em>
             (application only) <br>This submenu's options allow the
             inclusion or exclusion of non-positional sequence features
@@ -485,7 +483,13 @@
       </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
           for a description of all colour schemes.
       </em><br></li>
-      <li><strong>By Conservation<br>
+        <li><strong>Sequence ID<br></strong><em>Shades
+            sequences using their Sequence ID colour. Useful when
+            performing <a
+            href="../calculations/treeviewer.html#partitioning">tree
+              based subfamily analysis</a>.
+        </em></li>
+        <li><strong>By Conservation<br>
       </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
             by Conservation</a>.
       </em><br></li>
@@ -579,28 +583,26 @@
       is 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>'Trim Retrieved Sequences' - when checked, Jalview
-              will discard any additional sequence data for accessions
-              associated with sequences in the alignment. <br> <strong>Note:
-                Disabling this could cause out of memory errors when
-                working with genomic sequence records !</strong><br> <strong>Added
-                in Jalview 2.8.1</strong>
-            </li>
-            <li>'Standard Databases' will check sequences against
-              the EBI databases plus any active DAS sequence sources</li>
-          </ul> Other sub-menus allow you to pick a specific source to query
-          - sources are listed alphabetically according to their
-          nickname.
-      </em><br></li>
-    </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. those provided by
+						EMBL-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>'Trim Retrieved Sequences' - when checked, Jalview will
+								discard any additional sequence data for accessions associated
+								with sequences in the alignment. <br> <strong>Note:
+									Disabling this could cause out of memory errors when working
+									with genomic sequence records !</strong><br> <strong>Added
+									in Jalview 2.8.1</strong>
+							</li>
+							<li>'Standard Databases' will check sequences against the
+								EBI databases.</li>
+						</ul> Other sub-menus allow you to pick a specific source to query -
+						sources are listed alphabetically according to their nickname.
+				</em><br></li>
+			</ul>
     <p>Selecting items from the following submenus will start a
       remote service on compute facilities at the University of Dundee,
       or elsewhere. You need a continuous network connection in order to