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NI boards have separate clocks for AI, AO and digital IO with ability to define waveforms for each and synchronize them if desired. Able to internally by software, reroute signals such that a counter output appears on a different pin. Or route a specific pin for use as analog reference trigger...

While expensive, DAQ hardware and LabVEW software from National Instruments offers top notch software and hardware with terrific responsive technical support. Accurate low noise DAQ with software ability to configure and control it down to very low level tasks is available. Steve