sequence alignments and EPS files.
</li>
<li>The <a href="#editing"><strong>"Editing"</strong>
- Preferences</a> tab contains settings affecting the export of
- sequence alignments and EPS files.
+ Preferences</a> tab contains settings affecting the behaviour of alignments as you edit them.
+ </li>
+ <li>The <a href="#hmmer"><strong>"HMMER"</strong>
+ Preferences</a> tab allows you to configure locally installed HMMER tools.
</li>
<li>The <a href="../webServices/webServicesPrefs.html"><strong>"Web
Service"</strong> Preferences</a> tab allows you to configure the <a
<em>Sort with New Tree</em> - When selected, any trees calculated or
loaded onto the alignment will automatically sort the alignment.
</p>
- <p> </p>
- <p> </p>
+ <p>
+ <a name="hmmer"><strong>"HMMER" 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>