Yes. The Jalview Desktop has a number of command line options, and recent versions of the Jalview Desktop application come with a command line tool ‘jalview’ that allows you to call it from the command line.

Open a command prompt or terminal and try:

jalview -help

This should list the current set of arguments Jalview supports. The online documentation also includes a list of jalview command line parameters

Note: This FAQ has been updated - we no longer recommend the -Djava.ext.dirs=lib argument since it prevents Jalview from accessing some web services, and will be disabled in future versions of Java.