A state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. MSAProbs can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. MSAProbs-MPI is a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20.