-<html>\r
-<head>\r
-<title>Multiple Sequence Alignment Web Service</title>\r
-</head>\r
-<body>\r
-<strong>Multiple Sequence Alignment Web Services</strong>\r
-<p>\r
-Multiple sequence alignment services are accessed from the <strong>Web\r
-Service→Alignment</strong> menu. When an entry from this menu is\r
-selected, either the currently selected residues, or the whole\r
-sequence set (if there is no selection or only one sequence is\r
-selected) will be submitted for multiple sequence alignment.\r
-</p>\r
-<p>There are two kinds of multiple sequence alignment operations\r
-available:<ul>\r
-<li><em>alignment</em> - where a new alignment is constructed from the input\r
-</li>\r
-<li><em>realignment</em> -\r
-where any existing alignments in the input are passed to the service\r
-for profile based alignment.\r
-</li>\r
-</ul>\r
-</p>\r
-<p>\r
-<strong>Multiple Alignments of Sequences with hidden columns</strong><br>\r
-Multiple alignment services are 'column separable' analysis\r
-operations. If the input contains <a\r
-href="../features/hiddenRegions.html">hidden columns</a> then each\r
-visible segment of the input sequence set will be submitted for\r
-alignment separately, and the results concatenated (with the hidden\r
-regions preserved) once all alignment functions have completed. Each\r
-sub-job's state is reported in its own tab:\r
-<p><center><strong>Multiple Multiple Sequence Alignment sub jobs running at\r
-once</strong><center></p>\r
-<center><img src="multimafftjbs.gif" align="centre"></center>\r
-</p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Multiple Sequence Alignment Web Service</title>
+</head>
+<body>
+ <strong>Multiple Sequence Alignment Web Services</strong>
+ <p>
+ Multiple sequence alignment services are accessed from the <strong>Alignment</strong>
+ submenu of the Alignment Window's <strong>Web Service</strong> menu.
+ When an entry from one of these menus is selected, either the
+ currently selected residues, or the whole sequence set (if there is
+ no selection or only one sequence is selected) will be submitted for
+ multiple sequence alignment.
+ </p>
+ <p>There are two kinds of multiple sequence alignment operations
+ available:
+ <ul>
+ <li><em>alignment</em> - where a new alignment is constructed
+ from the input</li>
+ <li><em>realignment</em> - where any aligned sequences will be
+ used by the service to construct a profile based alignment of the
+ remaining unaligned sequences</li>
+ </ul>
+ <strong>JABAWS Alignment services</strong>
+ <br> Most alignment services are provided by the
+ <a href="JABAWS.html">JABAWS framework</a>, which allows you to
+ customise the precise parameters used when running each alignment
+ program. In addition to the 'Default settings', you may choose from a
+ range of alignment preset settings, or create your own using the
+ <a href="webServicesParams.html">'Edit Settings And Run ..' dialog
+ box</a>.
+ </p>
+ <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>
+ <li><a href="http://www.clustal.org/">Clustal Omega and
+ Clustal W</a> (version 2.0.12)</li>
+ <li><a href="http://mafft.cbrc.jp/alignment/software/">Mafft</a>
+ (version 6.8.57b)</li>
+ <li><a href="http://www.drive5.com/muscle">Muscle</a> (version
+ 3.8.31)</li>
+ <li><a
+ href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a>
+ (version 8.99)</li>
+ <li><a href="http://probcons.stanford.edu/">Probcons</a>
+ (version 1.12)</li>
+ </ul>
+ </p>
+
+ <p>
+ <strong>Multiple Alignments of Sequences with hidden
+ columns</strong><br> Multiple alignment services are 'column
+ separable' analysis operations. If the input contains <a
+ href="../features/hiddenRegions.html">hidden columns</a> then
+ each visible segment of the input sequence set will be submitted for
+ alignment separately, and the results concatenated (with the hidden
+ regions preserved) once all alignment functions have completed. Each
+ sub-job's state is reported in its own tab:
+ <p>
+ <center>
+ <strong>Multiple Multiple Sequence Alignment sub jobs
+ running at once</strong>
+ <center>
+ </p>
+ <center>
+ <img src="multimafftjbs.gif" align="centre">
+ </center>
+ </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff