6.1.3 Programming Options
Atmel Studio supports programming of Atmel AVR devices using the Atmel AVR JTAGICE mkII. The programming dialog can be configured to use JTAG, aWire, SPI, or PDI modes, according to the target device selected.
The clock frequency can only be configured for the SPI interface. For JTAG, aWire, and PDI interfaces, programming is done independently of the target's clock, so no configuration is required.