--- /dev/null
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+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
+ * 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.
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+ * Jalview is distributed in the hope that it will be useful, but
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+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
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+ * 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>Multi-Group Sequence Harmony and Multi-Relief</title>
+</head>
+<body>
+ <strong>Functional residue analysis with Sequence Harmony and
+ Multi-Relief</strong>
+ <p>
+ The Sequence Harmony and Multi-Relief (SHMR) service (<a
+ href="#shmrref">Brandt, Feenstra and Heringa, 2010</a>) available
+ from the <em>Analysis</em> sub-menu of the alignment window's web
+ services menu provides a method for the identification of significant
+ patterns of <em>sub-family variation</em> amongst the columns of an
+ alignment.
+ </p>
+ <p>
+ <strong>Instructions for use</strong><br> The service requires a
+ protein sequence multiple alignment that has been sub-divided into
+ groups containing at least two non-identical protein sequences. An
+ easy way to create groups is to use the built-in <a
+ href="../calculations/tree.html">neighbour-joining or UPGMA tree</a>
+ routines to calculate a tree for the alignment, and then click on the
+ tree to subdivide the alignment.
+ </p>
+ <p>
+ The SHMR service operates on the currently selected visible region(s)
+ of the alignment. Once submitted, a job progress window will display
+ status information about your job, including a URL which allows you to
+ visit the status page on the
+ <a href="http://www.ibi.vu.nl/programs/shmrwww/">IBIVU SHMR server</a>.
+ </p>
+ <p>When the job is complete, Jalview will automatically open a new
+ window containing the alignment and groups that were submitted for
+ analysis, with additional histograms added portraying the SHMR scores
+ for each column of the sub-grouped alignment.</p>
+ <p>
+ If you use this service in your work, please cite :<br /><a name="shmrref"/> Brandt,
+ B.W.*, Feenstra, K.A*. and Heringa, J. (2010) Multi-Harmony: detecting
+ functional specificity from sequence alignment. <a
+ href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415">Nucleic
+ Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
+ <p>
+ <strong><em>Note:</em></strong> The SHMR service is implemented with Jalview's RESTful
+ web service client, first introduced in Jalview 2.7.
+ </ul>
+ </p>
+</body>
+</html>
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