The Phylogenetic Tree of RNA Polymerase Constructed Using MOM Method

Phylogenetic analysis is a study of evolutionary relationship between organisms or species, and the evolutionary is displayed as a phylogenetic tree. In this paper, the phylogenetic tree was constructed by using distance-based method; UPGMA and the proposed method, MOM estimator. The UPGMA calculates the average of possible pairwise distances to get a new distance in the clustering process. If outliers exist in the possible pairwise distances, new mean distances are calculated, and the result is not robust. To overcome this problem, we implement a checking process to detect the outliers using MAD_n criteria on (based on median), and the new distances using the modified one-step M-estimator (MOM). In order to evaluate the branch of the tree constructed, the bootstrap method is used and the p-value (bootstrap value) for both methods is compared.