A Device Firmware Update based USB programmer for Atmel chips
dfu-programmer is an implementation of the Device Firmware Upgrade class USB driver that enables firmware upgrades for various USB enabled (with the correct bootloader) Atmel chips. This program was created because the Atmel FLIP program for flashing devices does not support flashing via USB on Linux, and because standard DFU loaders do not work for Atmel's chips.
Check out the Atmel website for more information. They are kind enough to provide generally correct specifications this implementation is based on.
The project website is http://dfu-programmer.sourceforge.net and you can use that to check for updates.