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- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
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+<head><title>ClustalW Alignment</title></head>
+<body>
+<p><strong>ClustalW Alignments</strong></p>
+<p>ClustalW is a program for multiple sequence alignment. It works
+with both DNA and protein sequences, and can also perform profile
+profile alignments to align two or more multiple sequence
+alignments.</p>
+<p>
+Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) <br>
+CLUSTAL W: improving the sensitivity of progressive multiple
+sequence alignment through sequence weighting, position specific gap
+penalties and weight matrix choice.<br>
+<em>Nucleic Acids Research</em> <strong>22</strong> 4673-4680
+</p>
+<p>There are two versions of this alignment function, which will operate
+on the selected region, if any, or the whole sequence set:</p>
+<ul>
+ <li><strong>Web Service→Alignment→ClustalW Multiple Sequence Alignment</strong><br>
+ Aligns using the clustalW program, ignoring any gaps in the submitted sequence
+ set. </li>
+ <li><strong>Web Service→Alignment→ClustalW Mulitple Sequence Alignment
+ Realign </strong><br>
+ Submits the sequences with existing gaps to clustalW, which will preserve
+ existing gaps and re-align those regions which are not optimal. </li>
+</ul>
+<em>As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.</em>
+</body>
+</html>
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