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A cluster tool that consists of several processing modules, a transport robot, and loadlocks is widely used for wafer processing in the semiconductor industry. The cluster tool repeats an identical operational sequence for processing wafers in a lot, and such a cyclic operation sequence is determined by the wafer flow pattern and process times of a wafer lot. When a wafer lot changes, the tool operation sequence should be switched accordingly. Switching from a cyclic tool operation sequence to another is subject to deadlocks and unnecessary task delays to avoid scheduling complexity. Hence, it is necessary to have a scheduling method for such frequent lot switchings that prevents a deadlock and reduces the switching time. In this paper, we first develop a Petri net model for lot switching operations and then utilize a mixed integer programming model for an optimal schedule. However, since its practical value is limited, we develop effective heuristic methods for lot switching in single-armed and dual-armed cluster tools. The scheduling strategies adapt prevalent cyclic tool scheduling rules, such as backward and swap sequences. By computational experiments, we prove the efficiency and effectiveness of the proposed scheduling rules.