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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
*
* This file is part of Jalview.
*
The majority of these scores were described by Valdar in 2002
(Scoring residue conservation. <em>Proteins: Structure,
Function, and Genetics</em> 43(2): 227-241. <a
- href="http://www.ncbi.nlm.nih.gov/pubmed/12112692"
- >PubMed</a> or available on the <a
- href="http://www.well.ox.ac.uk/~valdar/publications.html"
- >Valdar Group publications page</a>), but the SMERFs score was
- developed later and described by Manning et al. in 2008 (<a
- href="http://www.biomedcentral.com/1471-2105/9/51"
- >BMC Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
+ href="http://www.ncbi.nlm.nih.gov/pubmed/12112692">PubMed</a>
+ or available on the <a
+ href="http://valdarlab.unc.edu/publications.html">Valdar
+ Group publications page</a>), but the SMERFs score was developed later
+ and described by Manning et al. in 2008 (<a
+ href="http://www.biomedcentral.com/1471-2105/9/51">BMC
+ Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51</a>).
</p>
<p>
<strong>Enabling and disabling AACon calculations</strong><br />
<strong>Configuring which AACon calculations are performed</strong><br />
The <strong>Web Services→Conservation→Change
AACon Settings ...</strong> menu entry will open a <a
- href="webServicesParams.html"
- >web services parameter dialog</a> for the currently configured AACon
- server. Standard presets are provided for quick and more expensive
- conservation calculations, and parameters are also provided to
- change the way that SMERFS calculations are performed.<br /> <em>AACon
- settings for an alignment are saved in <a
- href="../features/jalarchive.html"
- >Jalview projects</a> along with the latest calculation results.
+ href="webServicesParams.html">web services parameter
+ dialog</a> for the currently configured AACon server. Standard presets
+ are provided for quick and more expensive conservation calculations,
+ and parameters are also provided to change the way that SMERFS
+ calculations are performed.<br /> <em>AACon settings for an
+ alignment are saved in <a href="../features/jalarchive.html">Jalview
+ projects</a> along with the latest calculation results.
</em>
</p>
<p>