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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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
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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/>.
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+<head>
+<title>Multiple Sequence Alignment Web Service</title>
+</head>
+<body>
+<strong>Multiple Sequence Alignment Web Services</strong>
+ <p>
+ Multiple sequence alignment services are accessed from the <strong>Alignment</strong>
+ submenu of the Alignment Window's <strong>Web Service</strong> menu.
+ When an entry from one of these menus is selected, either the
+ currently selected residues, or the whole sequence set (if there is no
+ selection or only one sequence is selected) will be submitted for
+ multiple sequence alignment.
+ </p>
+ <p>There are two kinds of multiple sequence alignment operations
+available:
+<ul>
+ <li><em>alignment</em> - where a new alignment is constructed from
+ the input</li>
+ <li><em>realignment</em> - where any aligned sequences will be
+ used by the service to construct a profile based alignment of the
+ remaining unaligned sequences.</li>
+</ul>
+ <strong>JABAWS Alignment services</strong><br> Most alignment services are
+ provided by the
+ <a href="JABAWS.html">JABAWS framework</a>, which allows you to
+ customise the precise parameters used when running each alignment
+ prgoram. In addition to the 'Default settings', you may choose from a
+ range of alignment preset settings, or create your own using the
+ <a href="webServicesParams.html">'Edit Settings And Run ..' dialog
+ box</a>.
+ </p>
+ <p><strong>Alignment programs supported by JABAWS</strong><ul>
+ <li><a href="http://www.clustal.org/">ClustalW</a> (version 2.0.12)</li>
+ <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.713)</li>
+ <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.7) </li>
+ <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.14) </li>
+ <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
+ </ul>
+</p>
+
+<p><strong>Multiple Alignments of Sequences with hidden
+columns</strong><br>
+Multiple alignment services are 'column separable' analysis operations.
+If the input contains <a href="../features/hiddenRegions.html">hidden
+columns</a> then each visible segment of the input sequence set will be
+submitted for alignment separately, and the results concatenated (with
+the hidden regions preserved) once all alignment functions have
+completed. Each sub-job's state is reported in its own tab:
+<p>
+<center><strong>Multiple Multiple Sequence Alignment
+sub jobs running at once</strong>
+<center>
+</p>
+<center><img src="multimafftjbs.gif" align="centre"></center>
+</p>
+</body>
+</html>