3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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>
25 Multiple sequence alignment services are accessed from the <strong>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
28 currently selected residues, or the whole sequence set (if there is no
29 selection or only one sequence is selected) will be submitted for
30 multiple sequence alignment.
32 <p>There are two kinds of multiple sequence alignment operations
35 <li><em>alignment</em> - where a new alignment is constructed from
37 <li><em>realignment</em> - where any aligned sequences will be
38 used by the service to construct a profile based alignment of the
39 remaining unaligned sequences.</li>
41 <strong>JABAWS Alignment services</strong><br> Most alignment services are
43 <a href="JABAWS.html">JABAWS framework</a>, which allows you to
44 customise the precise parameters used when running each alignment
45 prgoram. In addition to the 'Default settings', you may choose from a
46 range of alignment preset settings, or create your own using the
47 <a href="webServicesParams.html">'Edit Settings And Run ..' dialog
50 <p><strong>Alignment programs supported by JABAWS</strong>. <br/>Versions shown are those bundled with JABAWS 2.01 - if you are using a different server, check its home page to find out which versions are provided.<ul>
51 <li><a href="http://www.clustal.org/">Clustal Omega and Clustal W</a> (version 2.0.12)</li>
52 <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.8.57b)</li>
53 <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>
54 <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>
55 <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
59 <p><strong>Multiple Alignments of Sequences with hidden
61 Multiple alignment services are 'column separable' analysis operations.
62 If the input contains <a href="../features/hiddenRegions.html">hidden
63 columns</a> then each visible segment of the input sequence set will be
64 submitted for alignment separately, and the results concatenated (with
65 the hidden regions preserved) once all alignment functions have
66 completed. Each sub-job's state is reported in its own tab:
68 <center><strong>Multiple Multiple Sequence Alignment
69 sub jobs running at once</strong>
72 <center><img src="multimafftjbs.gif" align="centre"></center>