The phylogenetic tree is a widely-used tool to show the evolutionary relationship between taxa. There are many types of phylogenetic trees proposed in the literature such as maximum likelihood, neighbor-joining, and UPGMA trees. The topologies of different types of trees are not the same. Even for the same type of tree, the topologies are different when they embed different nucleotide substitution models, such as the JC69 model, K80 model, TN93 model, and so on. Although each type of tree has its advantages, selecting a suitable tree among these choices becomes a challenging problem. In this study, we propose a method based on testing the nucleotide substitution number between sequences to select trees. An Ebolavirus example is used to illustrate the method. In addition, this approach can select a suitable nucleotide substitution model for a particular type of tree. For this ebolavirus example, the JC69 model is the selected substitution model for the maximum likelihood tree.