Multi-tier message correlation

A system and method determines correlations within multi-tier communications based on repeated iterations/episodes of executions of a target application. Content-based correlations are determined by encoding the content using a finite alphabet, then searching for similar sequences among the multiple traces. By encoding the content to a finite alphabet, common pattern matching techniques may be used, including, for example, DNA alignment algorithms. To facilitate alignment of the traces, structural and/or semantic breakpoints are defined, and the encoding in each trace is synchronized to these breakpoints. To facilitate efficient processing, a hierarchy of causality among tier-pairs is identified, and messages at lower levels are ranked and temporally filtered, based on activity intervals at higher levels of the hierarchy.