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The purpose of this study was to investigate the use of decision tree for the classification of antimicrobial peptides. The classification was based on the activities of known antimicrobial peptides against comon microbes including Escherichia coli and Staphylococcus aureus. A feature selection was employed to select an effective subset of features from available attribute sets. Sequential applications of decision tree with 17 nodes with 9 leaves and 13 nodes with 7 leaves provided the E. coli and S. aureus, respectively. Angle subtended by positively charged face and the positive charge comonly gave higher acuracies in both E. coli and S. aureus datasets. In this study, we describe a successful application of decision tre that provides the understanding of the effects of physicochemical characteristics of peptides on bacterial membrane.