Here is a good, cheap alternative to be used with FMS software that was mentioned above

http://cgi.ebay.com/RC-Flight-Simula...QQcmdZViewItem

now you cant hook up your controller through this but it works....

Otherwise, you'd need a cable to hookup your Transmitter to the computer so it can work with FMS. You will need something like
http://cgi.ebay.com/FMS-Simulator-US...QQcmdZViewItem

IT will work with both JR and Futaba.