Add info on new programs

diff --git a/website/index.html b/website/index.html
index eca1691..4dd5d80 100644 (file)
--- a/website/index.html
+++ b/website/index.html
@@ -47,9 +47,10 @@ is free software which provides <a href="http://en.wikipedia.org/wiki/Web_servic
 include <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
 <a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, \r
 <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. Analysis services allow\r
-prediction of protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, \r
+prediction of the protein secondary structure with <a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, \r
 <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> and <a href="http://globplot.embl.de/">GlobPlot</a>; \r
-and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>.  \r
+and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. The secondary structure for an RNA aligment is possible with \r
+the RNAalifold program from the <a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.\r
 </p><p> \r
 <span style="color:black; font-weight:normal; text-align:left;">\r
 JABA 2.1 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) and the <strong>JABAWS command-line client</strong>, and provide multiple alignment \r

diff --git a/website/man_about.html b/website/man_about.html
index a1c5375..46a7134 100644 (file)
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+++ b/website/man_about.html
@@ -112,6 +112,11 @@
   <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
   <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
 </ul>\r
+<p>Protein Secondary structure</p>\r
+<ul>\r
+  <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/www-jpred">Jpred</a></span> (3.0.3) </li>\r
+</ul>\r
+\r
 <p>Protein disorder prediction</p>\r
 <ul>\r
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>\r
@@ -119,10 +124,14 @@
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>\r
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://globplot.embl.de/">GlobPlot</a></span> (2.3) </li>\r
   </ul>\r
-<p>Amino Acid conservation </p>\r
+<p>Amino Acid conservation</p>\r
 <ul>\r
   <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a></span> (1.0) </li>\r
 </ul>\r
+<p>Secondary structure for an RNA aligment</p>\r
+<ul>\r
+  <li><span style="color:black; font-weight:normal; text-align:left;">RNAalifold from <a href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a></span> (2.0) </li>\r
+</ul>\r
 \r
 \r
 \r