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If by "whole building simulation" you mean annual energy performance of the HVAC and other systems serving the building, then EnergyPlus may be the only choice. WUFI is probably better for a study focused mainly on moisture performance of the envelope. The model in EnergyPlus was similiar to 1-D WUFI at the time HAMT was added. Because of a lack of input data for materials, HAMT has not really been used all that much and it should be used with caution and probably checked against WUFI.