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+<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
+ prgoram. 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://align.bmr.kyushu-u.ac.jp/mafft/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>