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The infrared (IR) guided missiles (G/M) which is equipped with pulse width modulated (PWM) seeker are present in inventory of various countries. Especially air platforms use flares to protect itself from such kind of G/M's. But the efficiency of the flare launching program is dependent on the type of the flares and their launching times. In this paper the process of determination of the flare type and flare launching time parameters in flare launching program via hidden Markov models (HMM) will be investigated.