JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / help / html / webServices / AACon.html

diff --git a/help/html/webServices/AACon.html b/help/html/webServices/AACon.html
index 5dd4472..5cec67d 100644 (file)
--- a/help/html/webServices/AACon.html
+++ b/help/html/webServices/AACon.html
@@ -30,13 +30,13 @@
     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 />
@@ -49,14 +49,13 @@
     <strong>Configuring which AACon calculations are performed</strong><br />
     The <strong>Web Services&rarr;Conservation&rarr;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>