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<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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* This file is part of Jalview.
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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>
+ 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
+ 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>.
<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>
+ <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>
+ 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>
<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:
+ 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