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The Air Force SEEK EAGLE Office (AFSEO), Eglin Air Force Base (AFB), FL, is the United States Air Force (USAF) authority for weapons certification efforts. AFSEO performs test and evaluation for aircraft/store compatibility certification and uses computational fluid dynamics (CFD) to support this process. Determining the flow about an aircraft/store combination can be extremely difficult. Complicated geometry such as pylons, launchers, and internal weapons bays can create severe acoustic and aerothermodynamic environments, which are challenging to numerically simulate. The additional challenge of rapidly and accurately simulating the trajectory of a store separation in a high-volume simulation environment is beyond the capabilities of most CFD programs. The USAF requirement for numerous, simultaneous and quick-reaction solutions for a wide variety of stores and aircraft can only be accomplished through application of parallel high-performance computing resources that meet the significant computational and memory demands of the various cases. This project increases combat capability for the current USAF fleet of tactical and strategic aircraft with associated weapon systems. Before operational use, all aircraft/store configurations must be certified for safe loading, carriage and jettison/release. AFSEO provides flight certification recommendations, which are based on combinations of engineering analysis, ground, and flight testing. Engineering analyses come from disciplines in carriage loads, store separations, flutter, ballistics, stability and control, and electromagnetic compatibility and interference. The AFSEO CFD team provides time-critical support for engineering analyses - in the form of computed aircraft/store carriage aerodynamic loads, predicted store separation characteristics, and visualized flow field physics - used to optimize the application of ground and flight testing, reducing risk and lowering cost of fielding new weapons. This paper discusses four of the most recently applied AFSEO CFD tasks and code development, related to specific aircraft/store certifications.