-<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>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>
-</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>
+ <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>