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/>.
20 <title>Multiple Sequence Alignment Web Service</title>
23 <strong>Multiple Sequence Alignment Web Services</strong>
24 <p>Multiple sequence alignment services can be accessed from either
25 the <strong>Alignment</strong> or the <strong>JABAWS Alignment</strong>
26 submenu of the Alignment Window's <strong>Web Service</strong> menu.
27 When an entry from one of these menus is selected, either the currently
28 selected residues, or the whole sequence set (if there is no selection
29 or only one sequence is selected) will be submitted for multiple
30 sequence alignment.</p>
31 <p>There are two kinds of multiple sequence alignment operations
34 <li><em>alignment</em> - where a new alignment is constructed from
36 <li><em>realignment</em> - where any aligned sequences will be
37 used by the service to construct a profile based alignment of the
38 remaining unaligned sequences.</li>
40 The <a href="JABAWS.html">JABAWS Alignment services</a> also offer a
41 range of predefined alignment settings and the opportunity for you to
42 define your own set of parameters for running the alingment program.</p>
43 <p><strong>Multiple Alignments of Sequences with hidden
45 Multiple alignment services are 'column separable' analysis operations.
46 If the input contains <a href="../features/hiddenRegions.html">hidden
47 columns</a> then each visible segment of the input sequence set will be
48 submitted for alignment separately, and the results concatenated (with
49 the hidden regions preserved) once all alignment functions have
50 completed. Each sub-job's state is reported in its own tab:
52 <center><strong>Multiple Multiple Sequence Alignment
53 sub jobs running at once</strong>
56 <center><img src="multimafftjbs.gif" align="centre"></center>