Find signal phase shift

[juswaitn]

I need to test amplifiers to verify the input signal is in phase with the output signal. I am using an USB-6212 to output a square wave to the input of the amp. I am using the analog input to read the output of the amp (through a divider). Without using external hardware, I am at a loss on how to go about doing this.  

[RobertoBozzolo]

An option could be to acquire the square wave as well as amplifier output signal and search for zero crossing of both signals to quantify the phase shift.