A Physical Error Estimation Tool (PEET) is introduced in Matlab for predicting physical gate errors of quantum information processing (QIP) operations by constructing and then simulating gate sequences for a wide variety of user-defined, Hamiltonian-based physical systems. PEET is designed to accommodate the interdisciplinary needs of quantum computing design by assessing gate performance for users familiar with the underlying physics of QIP, as well as those interested in higherlevel computing operations. The structure of PEET separates the bulk of the physical details of a system into Gate objects, while the construction of quantum computing gate operations are contained in GateSequence objects. Gate errors are estimated by Monte Carlo sampling of noisy gate operations. The main utility of PEET, though, is the implementation of QuantumControl methods that act to generate and then test gate sequence and pulse-shaping techniques for QIP performance. This work details the structure of PEET and gives instructive examples for its operation.