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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>
+ <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>
+ <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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