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[jalview.git] / help / html / webServices / index.html
diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index de04ec1..6b5c5e1 100755 (executable)
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -2,9 +2,9 @@
         <head><title>Web Services</title></head>\r
         <body>\r
         <p><strong>Web services</strong></p>\r
-        <p>A variety of web services are available from the Alignment window's\r
-          <strong>Calculations&#8594;Web Service</strong> menu.\r
-            </p>\r
+        \r
+<p>A variety of web services are available from the Alignment window's <strong> \r
+  Web Service</strong> menu. </p>\r
             <p>Jalview's distributed computations are SOAP based services exposing\r
               protein sequence alignment and secondary structure prediction programs. These services actually run\r
                 on the cluster based in the School of Life Sciences, University of\r
@@ -21,17 +21,33 @@
                   possible for some services.\r
                   </p>\r
                   <p>Current services:\r
-                  <ul>\r
-                  <li>ClustalW Multiple Alignment<br>\r
-                  The clustal W service remains one of the more popular Jalview features.\r
+                  <ul><a href="msaclient.html"><strong>Multiple\r
+                  Sequence Alignment Services</strong></a><ul>\r
+                  <li><a href="clustalw.html">ClustalW Multiple Alignment and re-alignment</a><br>\r
+                  The clustal W service remains one of the more\r
+                  popular Jalview features.\r
                   </li>\r
-                  <li>Muscle Multiple Alignment<br>\r
+                  <li><a href="muscle.html">Muscle Multiple Alignment</a><br>\r
                   High Quality and High Throughput multiple alignments of proteins. This\r
                   method can sometimes be more accurate than ClustalW when dealing with\r
                   diverse sets of sequences.\r
                   </li>\r
-                  <li>JNet Secondary Structure Prediction<br>\r
-                  <em>This is a front end to the existing JNet www server.</em>\r
+                  <li><a href="mafft.html">MAFFT</a><br>\r
+                  Multiple Alignment with Fast Fourier Transforms -\r
+                  a highly accurate and high throughput dna and amino\r
+                  acid alignment method, performing at least as well\r
+                  as ClustalW and Muscle.\r
+                  </li>\r
+                  </ul>                  \r
+                  </li>\r
+                  <li><strong>Secondary Structure Prediction</strong>\r
+                  <ul>\r
+                  <li><a href="jnet.html">JNet</a><br>This is a front end to the existing <a\r
+                  href="http://www.compbio.dundee.ac.uk/www-jpred/">JNet\r
+                  www server</a> allowing single sequence or profile\r
+                  based prediction.\r
+                  </li>\r
+                  </ul>\r
                   </li>\r
                   </ul>\r
                   </p>\r