Sending sine wave from MATLAB and reading on Arduino Uno
No, you can't. The Arduino Uno has no analog outputs to start with and,
as you guessed, it cannot run two programs at the same time.

Maybe you should search for a solution of the initial problem instead.
You should be aware that you cannot get consistent timings with
analogRead(). You will have to read the datasheet of the ATmega328p,
especially the section dedicated to the ADC. Then you will configure the
ADC yourself, at the register level. It has a feature called
“auto-trigger” which is intended to provide perfectly consistent
timings. This is what you are looking for.