I've got a decent knowledge of programming (incl. bash scripting) but I fail to understand how Arlequin works. Could you please help me with a very simple reproducible example on how to use Arlequin via the command line?

As the .zip file comes with its pre-compiled version, I'll just note that I'm on Mac OS X but of course, a reproducible example with Linux (or at worst with Windows) would also be helpful.