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This paper proposes a new algorithm (DEP-BDD) based on binary decision diagram (BDD) for reliability analysis of phased-mission systems (PMS) with multimode failures. DEP-BDD is a BDD-based combinatorial model which can be used to deal with more than one kind of dependences by applying dependence algebra, which is a generalization of phase algebra that handles more complex dependences. The nature of the BDD contributes the efficiency and low computational complexity of this algorithm. Two examples are analysed to illustrate the applications and advantages of our approach.