In this study, we have developed and implemented a systematic procedure for identifying and classifying macromolecular aggregates based on the powerful algorithms of graph theory. Our method is primarily intended to analyze MD trajectories, which usually contain thousands of particles. Indeed, their analysis is far from straightforward, which explains why traditional MD analysis tools do not directly provide information on these aggregates that may appear for short periods of time during the simulation. Moreover, as we will show, the top-down nature of our approach makes it generally applicable to any set of configurations, for instance, those arising from a systematic conformational search.