Muscle synergies provide a simple description of a complex motor control mechanism. Synergies are extracted from muscle activation patterns using factorisation methods. Despite the availability of several factorisation methods in the literature, the most appropriate method for muscle synergy extraction is currently unknown. In this study, we compared four muscle synergy extraction methods: non-negative matrix factorisation, principal component analysis, independent component analysis, and factor analysis. Probability distribution of muscle activation patterns were compared with the probability distribution of synergy excitation primitives obtained from the four factorisation methods. Muscle synergies extracted using non-negative matrix factorisation best matched the probability distribution of muscle activation patterns across different walking and running speeds. Non-negative matrix factorisation also best tracked changes in muscle activation patterns compared to the other factorisation methods. Our results suggest that non-negative matrix factorisation is the best factorisation method for identifying muscle synergies in dynamic tasks with different levels of muscle contraction.