The thesis proposed an amino acid substitution model for rotavirus, called ROTA for short. Analysis showed that ROTA differs from other existing models in both amino acid frequency vector and exchangeability coefficient matrix. When validated on a testing dataset, ROTA proved to be better than other model in reconstructing maximum likelihood phylogenetic trees. The thesis proposed an amino acid substitution model for rotavirus, called ROTA for short. Analysis showed that ROTA differs from other existing models in both amino acid frequency vector and exchangeability coefficient matrix. When validated on a testing dataset, ROTA proved to be better than other model in reconstructing maximum likelihood phylogenetic trees.