Computer programs (600, 700, 800, 900, 1000) and a programmed computer (1100) for automatically generating computer programs (i.e. sequences of instructions) are provided. The computer programs (600, 700, 800, 900, 1000) use Hidden Markov Models (400, 500) to generate sequences of program tokens, e.g., Gene Expression Programming chromosomes (100). Parameters of the Hidden Markov Models (400, 500) are numerically optimized, for example, by Differential Evolution with a goal of increasing the fitness of automatically generated programs.