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Many structural analyses of software systems are naturally formalized as relational queries, for example, the detection of design patterns, patterns of problematic design, code clones, dead code, and differences between the as-built and the as-designed architecture. This paper describes CrocoPat, an application-independent tool for relational programming. Through its efficiency and its expressive language, CrocoPat enables practically important analyses of real-world software systems that are not possible with other graph analysis tools, in particular analyses that involve transitive closures and the detection of patterns in graphs. The language is easy to use, because it is based on the well-known first-order predicate logic. The tool is easy to integrate into other software systems, because it is a small command-line tool that uses a simple text format for input and output of relations.