The use of probabilistic models of amino acid replacement is essential for the study of protein evolution, and programs like ProtTest implement different strategies to identify the best-fit model for the data at hand. For large protein alignments, this task can demand vast computational resources, preventing the justification of the model used in the analysis. We have implemented a High Performance Computing (HPC) version of ProtTest. ProtTest-HPC can be executed in parallel in HPC environments as: (1) a GUI-based desktop version that uses multi-core processors and (2) a cluster-based version that distributes the computational load among nodes. The use of ProtTest-HPC resulted in significant performance gains, with speedups of up to 50 on a high performance cluster.