+
+ <h2><a name="headlessmode"></a>Headless mode</h2>
+
+ <p>
+ Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the <code>--headless</code> argument. With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running. Most likely you will want to output another file, either an alignment for image file.
+ </p>
+ <p>
+ <strong>If you specify an argument for an output file</strong> (one or more of <code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then it will be assumed that you wish to <strong>run in headless mode</strong>.
+ </p>
+ <p>
+ You can force Jalview to run in graphical mode using the <code>--gui</code> or <code>--noheadless</code> arguments.
+ </p>
+
+ <p>
+ </p>
+
+