http://www.etas.com/en/products/inca_mip.php
So ETAS INCA is one of the leading software and hardware combinations. Competitors include ATI Vision, dSpace Control Desk and Vector CANape. They integrate directly with Matlab. Depending on the system, It's basically a prototype ECU that literally has real time access to every tuning parameter and can datalog at 1000 samples per second. Compare that to a Subaru Cobb Accessport which has maybe 10 real time maps and logs at like 10-15 samples per second. All the hardware ends up costing as much as a BRZ.
When the code is model-based in Matlab, it can be used easily in simulation packages to test if it works before it's used in an engine.