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Programs for the analysis of pathological voice data have been presented for the last few decades. Computerized Speech Lab (CSL) has been recognized as a standard in the field of pathological voice analysis. PRAAT is a new open program which is constantly being improved almost every week. CSL gives the "Voice disorders database" which was produced by Massachusetts Eye and Ear Infirmary. In this paper, we use PRAAT program for the analysis of voice data and compare the result of PRAAT with the result of CSL. We focus on the perturbation analysis on frequencies using several parameters like jitter, standard deviation of fundamental frequencies etc.