FANMOD

FANMOD, short for Fast Network Motif Discovery, is a software tool for identifying network motifs in biological and other complex networks. Network motifs are small subgraphs that occur in a network more often than expected by chance. FANMOD analyzes directed graphs (and can handle undirected networks) by comparing observed subgraph counts to those in randomized versions of the network.

The program uses fast enumeration of subgraphs up to a user-specified size (commonly 3 to 8 nodes) and, for large networks, Monte Carlo sampling to estimate motif frequencies. Randomized networks are generated by preserving the network's degree sequence through edge-switching or related methods. For each motif, FANMOD reports statistics such as counts in the real network, counts in randomized networks, z-scores, and p-values to indicate significance.

Input and output: input is typically an edge list or adjacency representation; output includes motif patterns and their statistics. It was designed to be faster than earlier tools for network motif discovery and has been widely used in systems biology to study transcriptional and regulatory networks, metabolic networks, and protein interaction networks.

Limitations: results depend on the chosen null model and sampling approach; motif discovery remains computationally intensive for very large motif sizes or networks. As with other motif analyses, interpretation should consider network context and methodological assumptions.