3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
4 * Copyright (C) 2014 The Jalview Authors
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
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Multiple Sequence Alignment Web Service</title>
26 <strong>Multiple Sequence Alignment Web Services</strong>
28 Multiple sequence alignment services are accessed from the <strong>Alignment</strong>
29 submenu of the Alignment Window's <strong>Web Service</strong> menu.
30 When an entry from one of these menus is selected, either the
31 currently selected residues, or the whole sequence set (if there is no
32 selection or only one sequence is selected) will be submitted for
33 multiple sequence alignment.
35 <p>There are two kinds of multiple sequence alignment operations
38 <li><em>alignment</em> - where a new alignment is constructed from
40 <li><em>realignment</em> - where any aligned sequences will be
41 used by the service to construct a profile based alignment of the
42 remaining unaligned sequences.</li>
44 <strong>JABAWS Alignment services</strong><br> Most alignment services are
46 <a href="JABAWS.html">JABAWS framework</a>, which allows you to
47 customise the precise parameters used when running each alignment
48 prgoram. In addition to the 'Default settings', you may choose from a
49 range of alignment preset settings, or create your own using the
50 <a href="webServicesParams.html">'Edit Settings And Run ..' dialog
53 <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>
54 <li><a href="http://www.clustal.org/">Clustal Omega and Clustal W</a> (version 2.0.12)</li>
55 <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.8.57b)</li>
56 <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>
57 <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>
58 <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
62 <p><strong>Multiple Alignments of Sequences with hidden
64 Multiple alignment services are 'column separable' analysis operations.
65 If the input contains <a href="../features/hiddenRegions.html">hidden
66 columns</a> then each visible segment of the input sequence set will be
67 submitted for alignment separately, and the results concatenated (with
68 the hidden regions preserved) once all alignment functions have
69 completed. Each sub-job's state is reported in its own tab:
71 <center><strong>Multiple Multiple Sequence Alignment
72 sub jobs running at once</strong>
75 <center><img src="multimafftjbs.gif" align="centre"></center>