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We define the real time trajectory generation problem to be how to generate, possibly with some delay, a full state space and input trajectory in real time from an output trajectory that is given online, while allowing a tradeoff between stability and performance. We propose two algorithms that solve the real time trajectory generation problem for flat systems with zero dynamics, and discuss some interesting properties. We explicitly address the tradeoff between stability and performance. The algorithms are validated in simulations and experiments with a thrust vectored ducted fan aircraft.