We present software tools for overcoming the problem of combinatorics in the enumeration of simple pathways and simple cycles in a first flow-through analysis of carbon transfer in large ecosystems. Rather than search through the very large number of potential routes in a reasonably sized ecosystem for the relatively small number of actual routes, our main algorithm performs an efficient rule-based construction of the actual routes. The enumeration of the unique pathways becomes tractable in terms of CPU time, which increases linearly with ecosystem size and connectedness. Networks of up to 80 entities can be evaluated using our software.