a protein sequence multiple alignment that has been sub-divided into
groups containing at least two non-identical protein sequences. An
easy way to create groups is to use the built-in <a
- href="../calculations/tree.html"
- >neighbour-joining or UPGMA tree</a> routines to calculate a tree for
- the alignment, and then click on the tree to subdivide the
- alignment.
+ href="../calculations/tree.html">neighbour-joining or
+ UPGMA tree</a> routines to calculate a tree for the alignment, and
+ then click on the tree to subdivide the alignment.
</p>
<p>
The SHMR service operates on the currently selected visible
region(s) of the alignment. Once submitted, a job progress window
will display status information about your job, including a URL
which allows you to visit the status page on the <a
- href="http://zeus.few.vu.nl/programs/shmrwww/"
- >IBIVU SHMR server</a>.
+ href="http://zeus.few.vu.nl/programs/shmrwww/">IBIVU SHMR
+ server</a>.
</p>
<p>When the job is complete, Jalview will automatically open a new
window containing the alignment and groups that were submitted for
analysis, with additional histograms added portraying the SHMR
scores for each column of the sub-grouped alignment.</p>
<p>
- If you use this service in your work, please cite :<br />
+ If you use this service in your work, please cite :<br />
<a name="shmrref" /> Brandt, B.W.*, Feenstra, K.A*. and Heringa, J.
(2010) Multi-Harmony: detecting functional specificity from sequence
alignment. <a
- href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415"
- >Nucleic Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
-
+ href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415">Nucleic
+ Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
<p>
<strong><em>Note:</em></strong> The Multi-Harmony service is
implemented with a prototype of Jalview's RESTful web service client