<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* 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/>.
---!>
+-->
<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>Web
-Service→Alignment</strong> menu. When an entry from this menu 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>Multiple sequence alignment services can be accessed from either
+the <strong>Alignment</strong> or the <strong>JABAWS 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 existing alignments in the input are passed to the service
-for profile based alignment.
-</li>
+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>
-</p>
+The <a href="JABAWS.html">JABAWS Alignment services</a> also offer a
+range of predefined alignment settings and the opportunity for you to
+define your own set of parameters for running the alingment program.</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>
-<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><strong>Multiple Multiple Sequence Alignment
+sub jobs running at once</strong>
+<center>
+</p>
<center><img src="multimafftjbs.gif" align="centre"></center>
</p>
</body>
git://source.jalview.org / jalview.git / blobdiff