PQMaker: Empirically estimating amino acid substitution models in a parallel environment

Amino acid substitution matrices are central to the model-based methods for reconstructing evolutionary trees from amino acid sequences. QMaker is an efficient method for estimating general time-reversible amino acid substitution matrices from a large biological dataset containing thousands of protein alignments using maximum likelihood principle. It allows researchers to build an amino acid substitution model on their own to best fit their subsequent phylogenetic analyses. In this work, we propose an approach to parallelize computation in QMaker, named pQMaker. Moreover, we provide an open-source message passing interface implementation for pQMaker (http://github.com/canhnd58/IQ-TREE/tree/pqmaker) built upon the latest IQ-TREE package. Experiments on benchmark data sets show that our implementation has significant speed gains compared with the original QMaker.