X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpreferences.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fpreferences.html;h=5bb0b8a84d4a913d05ecba9ea8003aa93a708672;hb=b5667f39acdf309cd92881b73edfda591e0acaf4;hp=8c6b699e00a56dfcd813392a4493069265425af9;hpb=9e31a59b947882325ffe614bd71fb732d7952a23;p=jalview.git

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 8c6b699..5bb0b8a 100755
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -64,6 +64,9 @@
     <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
         Preferences</a> tab contains settings affecting behaviour when editing alignments.
     </li>
+    <li>The <a href="#hmmer"><strong>&quot;HMMER&quot;</strong>
+        Preferences</a> tab allows you to configure locally installed HMMER tools.
+    </li>
     <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
           Service&quot;</strong> Preferences</a> tab allows you to configure the <a
       href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
@@ -382,7 +385,13 @@
     <em>Sort with New Tree</em> - When selected, any trees calculated or
     loaded onto the alignment will automatically sort the alignment.
   </p>
-  <p>&nbsp;</p>
-  <p>&nbsp;</p>
+  <p>
+    <a name="hmmer"><strong>&quot;HMMER&quot; Preferences tab</strong></a>
+  </p>
+  <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
+  then you should specify on this screen the location of the installation (the path to the folder 
+  containing binary executable programs). Double-click in the input field to open a file browser.</p>
+  <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
+  enabled in the Alignment window.</p>
 </body>
 </html>