Systems and methods for sequencing HVAC equipment of an HVAC system using data recorded in situ to build a model capable of making predictions about equipment efficiency and using that information, in combination with predictions about building load, to produce an operational sequence for the HVAC equipment that promotes an improved or optimized overall energy efficiency for the HVAC system. In one embodiment, the process is automated and utilizes Bayesian computational models or algorithms to generate are initial sequence. The process reduces engineering hours and may advantageously provide a means to predict potential sequencing problems for similar types of HVAC equipment.