<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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>.
</p>
<p>
<strong>Alignment programs supported by JABAWS</strong>. <br />Versions
- shown are those bundled with JABAWS 2.01 - if you are using a
+ 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/">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>
+ <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>
<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
git://source.jalview.org / jalview.git / blobdiff