The application of different substitution models to each gene (a.k.a. mixed model) should be considered in model-based phylogenetic analysis of multigene sequences. However, a single molecular evolution model is still usually applied. There are no computer programs able to conduct model selection for multiple loci at the same time, though several recently developed types of software for phylogenetic inference can handle mixed model. Here, I have developed computer software named ‘kakusan’ that enables us to solve the above problems. Major running steps are briefly described, and an analysis of results with kakusan is compared to that obtained with other program.