AVRDUDE is an utility to download/upload/manipulate the ROM and EEPROM contents of AVR microcontrollers using the in-system programming technique (ISP).
Uisp is a tool for AVR microcontrollers which can interface to many hardware in-system programmers.
$ sudo apt-get install binutils-avr gcc-avr avr-libc gdb-avr
See:
$ sudo apt-get install simulavr