-<html>\r
-<head><title>ClustalW Alignment</title></head>\r
-<body>\r
-<p><strong>ClustalW Alignments</strong></p>\r
-<p>ClustalW is a program for multiple sequence alignment. It works\r
-with both DNA and protein sequences, and can also perform profile\r
-profile alignments to align two or more multiple sequence\r
-alignments.</p>\r
-<p>\r
-Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) <br>\r
-CLUSTAL W: improving the sensitivity of progressive multiple\r
-sequence alignment through sequence weighting, position specific gap\r
-penalties and weight matrix choice.<br>\r
-<em>Nucleic Acids Research</em> <strong>22</strong> 4673-4680\r
-</p>\r
-<p>There are two versions of this alignment function, which will operate\r
-on the selected region, if any, or the whole sequence set:</p>\r
-<ul>\r
-<li><strong>Calculations→Web Service→Clustal\r
-Alignment..</strong><br>\r
-Aligns using the clustalW program, ignoring any gaps in the submitted\r
-sequence set.\r
-</li>\r
-<li><strong>Calculations→Web Service→Clustal\r
-Realign..</strong><br>\r
-Submits the sequences with existing gaps to clustalW, which will\r
-preserve existing gaps and re-align those regions which are not optimal.\r
-</li>\r
-</ul>\r
-</body>\r
-</html>\r
+#-------------------------------------------------------------------------------
+# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+# 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.
+#
+# 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/>.
+#-------------------------------------------------------------------------------
+<html>
+<!--
+ * 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>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>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff