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An automated system for resolving an intramuscular electromyographic (EMG) signal into its constituent motor unit potential trains (MUPTs) is presented. The system is intended mainly for clinical applications where several physiological parameters for each motor unit (MU), such as the motor unit potential (MUP) template and mean firing rate, are required. The system decomposes an EMG signal off-line by filtering the signal, detecting MUPs, and then grouping the detected MUPs using a clustering and a supervised classification algorithm. Both the clustering and supervised classification algorithms use MUP shape and MU firing pattern information to group MUPs into several MUPTs. Clustering is partially based on the K-means clustering algorithm. Supervised classification is implemented using a certainty-based classifier technique that employs a knowledge-based system to merge trains, detect and correct invalid trains, as well as adjust the assignment threshold for each train. The accuracy (93.2%±5.5%), assignment rate (93.9%±2.6%), and error in estimating the number of MUPTs (0.3±0.5) achieved for 10 simulated EMG signals comprised of 3-11 MUPTs are encouraging for using the system for decomposing various EMG signals.