Branch points arise in optical transmissions due to strong atmospheric turbulence, long propagation paths, or a combination of both. Unfortunately, these conditions are very often present in desired operational scenarios for laser weapon systems, optical communication, and covert imaging, which suffer greatly when traditional adaptive optics systems either cannot sense branch points or implement non-optimal methods for sensing and correcting branch points. In this research we create a MATLAB simulation of the real-time AO system at the Air Force Institute of Technology. Utilizing a selfreferencing interferometer as the high-order wavefront sensor-this type of sensor being theoretically immune to scintillation-this effort has extended previous theoretical work by adding realistic noise effects to the SRI's measurements before reconstructing the wavefronts and applying the control law. Previous research by Pellizzari presents a thorough analysis of various novel branch point tolerant reconstructors in the absence of noise. This study provides a foundation to guide hardware implementation in the future, where noise effects will be present.