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+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
<head><title>Web Service Menu</title></head>
<body>
<p><strong>Web Service Menu</strong></p>
-<p><strong><br>
- </strong> <em>Selecting one of the following menu items starts a remote service
- on compute facilities at the University of Dundee. You need a continuous network
- connection in order to use these services through Jalview. </em> </p>
<ul>
<li><strong>Fetch DB References</strong><br>
- <em>This will use the service WSDBFetch, provided by the EBI, to retrieve all
- uniprot database cross references and PDB ids associated with the selected sequences in
- the alignment if the sequences have valid Uniprot names or accession ids.</em><br>
+ <em>This will use 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 the sequence and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+ <br/>'Standard Databases' will check sequences against the EBI databases
+ plus any active DAS sequence sources, or you can verify against a specific
+ source from one of the sub-menus.</em><br>
+ </li>
+ <li><strong>Envision2 Services</strong><br/>
+ Submits one or more sequences, sequence IDs or database references to analysis workflows provided
+by the <a href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2
+web application</a>. This allows Jalview users to easily access the EnCore network of
+databases and analysis services developed by members of <a href="http://www.enfin.org">ENFIN</a>.
</li>
+ </ul>
+ </strong> <em>Selecting one of the following menu items starts a remote service
+ on compute facilities at the University of Dundee. You need a continuous network
+ connection in order to use these services through Jalview. </em> </p>
+ <ul>
<li><strong>Alignment</strong>
<ul>
<li><strong>ClustalW Multiple Sequence Alignment</strong><br>
with clustal W.</em></li>
<li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
<em> Submits the alignment or currently selected region for re-alignment
- with clustal W. Use this if you have added some new sequences to an existing
- alignment.</em></li>
+ with clustal W. This enables you to align more sequences to an existing alignment.</em></li>
<li><strong>MAFFT Multiple Sequence Alignment</strong><br>
<em>Submits all, or just the currently selected region for alignment with
MAFFT. </em> </li>