Methods for representing and evaluating dependency systems are provided. In one implementation a method is provided. The method includes receiving a file. The file includes a node array having data entries corresponding to one or more nodes. The file also includes an edge array having data entries corresponding to one or more edges, the edge entries identifying an invertability state of an edge, a suppressed state of an edge, and one or more partner edge linking a first and a second edge in the edge array. The method also include processing the received file. In another implementations a method for evaluating dependencies in a cyclic system is provided as well as a method for evaluating an enhanced directed dependency graph.