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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 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
+ <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
used by the service to construct a profile based alignment of the
remaining unaligned sequences.</li>
</ul>
-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>
+ <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.
git://source.jalview.org / jalview.git / blobdiff