Adam Packer wrote some LabVIEW software for acquiring and generating data from National Instruments cards called PackIO. It is meant to trigger and synchronize equipment as well as record any data, with a few specific modules for electrophysiology. The nice thing is that you can do just about everything in a hardware-timed fashion, so you’re limited only by the specifications of the NIDAQ card you choose.
Recorded data can be read in to MATLAB or Python using tools on this page.
Please check it out if you are in need of some well-vetted ‘master clock’ software. The program has been used in 30 papers in four different labs, and is available as open-source software at www.packio.org.