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Modeling and querying software repositories is an integral part of reverse engineering legacy software systems. Current data models and query languages for software repositories lack generality, extensibility, and sufficient formalism. In this paper, we propose an algebraic framework that provides both an extensible data model capable of modeling software information at multiple levels of abstraction, as well as an algebraic applicative query language that can be used effectively to express queries on the data model. We demonstrate the power of the algebraic framework by expressing a wide variety of queries drawn from reverse engineering literature. The algebraic approach combines issues of formal elegance, expressive power, and query processing and optimization within a single framework.