This thesis explores indirect estimation of distribution algorithms (IEDAs) for the evolution of tree structured expressions. Unlike conventional estimation of distribution algorithms, IEDAs maintain a distribution of the genotype space and indirectly search the solution space by performing a genotype-to-phenotype mapping.In this work we introduce two IEDAs named PDPE and N-gram GEP. PDPE induces a population of programs, encoded as fixed-length gene expression programming (GEP) chromosomes, by iteratively refining and randomly sampling a probability distribution of program instructions. N-gram GEP attempts to capture regularities in GEP chromosomes by sampling the probability distribution of triplet of instructions (3-grams).We tested the performance of these systems using a variety of non-trivial test problems, such as symbolic regression and the lawn-mower problem. We compared PDPE and N-gram GEP with their predecessors, probabilistic incremental program evolution (PIPE) and N-gram GP, and the canonical GEP algorithm. The results proved that our methodology is more efficient than PIPE and the canonical GEP algorithm.