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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
- 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 2.2 - 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/omega">Clustal Omega</a> (version 1.2.4)</li>
- <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.1)</li>
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 7.310)</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">T-coffee</a> (version 11.00.8cbe486)</li>
- <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
- <li><a href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>
- <li><a href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</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>
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