3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <head><title>ClustalW Alignment</title></head>
21 <p><strong>ClustalW Alignments</strong></p>
22 <p>ClustalW is a program for multiple sequence alignment. It works
23 with both DNA and protein sequences, and can also perform profile
24 profile alignments to align two or more multiple sequence
27 Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) <br>
28 CLUSTAL W: improving the sensitivity of progressive multiple
29 sequence alignment through sequence weighting, position specific gap
30 penalties and weight matrix choice.<br>
31 <em>Nucleic Acids Research</em> <strong>22</strong> 4673-4680
33 <p>There are two versions of this alignment function, which will operate
34 on the selected region, if any, or the whole sequence set:</p>
36 <li><strong>Web Service→Alignment→ClustalW Multiple Sequence Alignment</strong><br>
37 Aligns using the clustalW program, ignoring any gaps in the submitted sequence
39 <li><strong>Web Service→Alignment→ClustalW Mulitple Sequence Alignment
41 Submits the sequences with existing gaps to clustalW, which will preserve
42 existing gaps and re-align those regions which are not optimal. </li>
44 <em>As of Jalview 2.6, alignment services accessed via the 'Alignment' submenu should be considered legacy Jalview SOAP services.</em>