Chitra analyzes a program execution sequence (PES) collected during execution of a program and produces a homogeneous, semi-Markov chain model fitting the PES. The PES represents the evolution of a program state vector in time. Therefore Chitra analyzes the time-dependent behavior of a program. The paper describes a set of transforms that map a PES to a simplified PES. Because the transforms are program-independent, Chitra can be used with any program. Chitra provides a visualization of PES's and transforms, to allow a user visually to guide transform selection in an effort to generate a simple yet accurate semi-Markov chain model. The resultant chain can predict performance at program parameters different than those used in the input PES, and the chain structure can diagnose performance problems.