- <td><code>‑‑headless</code></td>
- <td>Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed.</td>
+ <td><code>‑‑headless / ‑‑noheadless</code></td>
+ <td>Run Jalview in headless (/ or not in headless) mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
+ <br/>
+ If you use a command line argument to specify an output file of some kind (<code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then <strong>headless mode will be assumed</strong>. If you don't want this behaviour use <code>--noheadless</code> or <code>--gui</code>.
+ </td>
+ </tr>
+
+ <tr valign="top">
+ <td><code>‑‑gui</code></td>
+ <td>Force Jalview to run in graphical mode. This can be used to counter the assumption of headless mode when an argument that creates an output file is used. <code>--gui</code> takes precedence over <code>--headless</code>.</td>