<body>
<p><strong>Preferences</strong></p>
+<p>The preferences panel is opened from the Jalview Desktop’s <strong><em>Tools</em></strong> menu.</p>
<p>There are six tabs in the Preferences dialog box:
<ul>
<li>The <a href="#visual"><strong>"Visual"</strong>
<p><em>Open file</em> - If this is selected then the default
alignment file will be opened when Jalview is started. You can change
the default file by clicking on file name and either typing in the file
-path or selecting it from the file chooser window.</p>
+path or selecting it from the file chooser window.<br/><em>Note: The default example alignment is updated periodically to demonstrate new features in Jalview.</em></p>
<p><a name="colours"><strong>"Colours" Preferences tab</strong></p>
<p><em>Alignment Colour</em> - The default colour scheme for a new alignment
window. If the chosen option is "User Defined" then the last