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We have developed a virtual integration environment (VIE) for the development of neural prosthetic systems. This paper, the second of two companion articles, describes the use of the VIE as a common platform for the implementation of neural decode algorithms. In this paper, a linear filter decode and a recursive Bayesian algorithm are implemented as separate signal analysis modules of the VIE for the real-time decode of end effector trajectory. The process of implementing each algorithm is described and the real-time behavior as well as computational cost for each algorithm is examined. This is the first report of the real-time implementation of the Mixture of Trajectory Models decode . These real-time algorithms can be easily interfaced with pre-existing modules of the VIE to control simulated and real devices.