A Method for Calculating the Least Mutated Sequence in DNA Alignment Based on Point Mutation Sites

It is hard to decide the root of a phylogenetic tree when no suitable outgroup sequence is available, especially in a high mutation rate system. Here we propose a bioinformatics method for calculating the least mutated sequence in DNA alignment based on point mutation sites. By parsimony principle, the least mutated sequence should be the ancestor (phylogenetic root) of the other sequences in an alignment result. The intuition suggests that our method would be sound only if enough sequences were collected. In this study, we used DNA mutation simulation data to test our method. The simulation results show that our method is very reliable and just a small proportion of sequences is required to find the least mutated sequence when the sampling is random. When the ancestral sequence is present in the dataset, the least mutated sequence calculated by our method is the ancestral sequence itself, i.e., the phylogenetic root of the dataset. When the ancestral sequence is not in the dataset, the least mutated sequence calculated by our method is the one closest to the phylogenetic root. Furthermore, the simulation demonstrates that our method is robust against reverse mutation and saturation mutation. The performance of our method improves with the increasing number of sequences. We developed the program based on this method which also calculates the transition/transversion ratio for each sequence in an DNA alignment. It can be used as a rough measure for estimating selection pressure and evolutionary stability for a sequence. In conclusion, our method and the corresponding programs could be a useful auxiliary tool for bioinformaticians and evolutionary biologists.