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AVR Atmel Programming Tools

You can use a bootloader to download a program to the MCU via UART but it is easier to just use a dedicated programmer. 

GNU Toolchain

If you have Ubuntu installed, all the GNU AVR tools can be found in the package manager.

Other Resources:
A C library to program various number of ATmega chips as well as abstract interfaces to set up timers, drive servos, read sensor data, etc..
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