+ <h3><a name="outputbehaviour"></a>Output behaviour</h3>
+
+ <h3><a name="overwrite"></a><code>--overwrite</code></h3>
+
+ <p>
+ By default, Jalview will refuse to overwrite an output file (alignment or image) unless backups are in operation (alignment files only). To force overwriting files, use the <code>--overwrite</code> argument.
+ </p>
+
+ <h3><a name="backups"></a><code>--backups / --nobackups</code></h3>
+
+ <p>
+ Jalview should honour your preferences for backup files of output alignment files. Using <code>--backups</code> or <code>--nobackups</code> forces the behaviour. With no backups set, you will need to use <code>--overwrite</code> to overwrite an existing file. Note that Jalview does not make backup files of exported images.
+ </p>
+
+ <h3><a name="mkdirs"></a><code>--mkdirs</code></h3>
+
+ <p>
+ If you want to output a file into a folder that doesn't yet exist (this might happen particularly when using <code>{dirname}</code> substitutions -- see below), then Jalview will fail to write the file since the parent directory doesn't exist. You can use <code>--mkdirs</code> to tell Jalview to make the new directory (or directories, it will create several nested directories if necessary) before writing the file. <code>--mkdirs</code> is cautious and will generally refuse to make a new directory using a relative path with <code>..</code> in.
+ </p>