GraphletCounter is a software tool for computing the graphlet signatures of nodes and motifs in biological networks. GraphletCounter can operate on its own or as a plugin to the network analysis environment Cytoscape. GraphletCounter computes the graphlet signatures of individual nodes or of motifs, which can be specified by files generated by the motif-finding tool mfinder. It displays graphlet signatures visually within Cytoscape, and can output graphlet data for integration with larger workflows. Graphlet signatures were introduced by the Przulj group at the University of California at Irvine; please see the following references:<p>Przulj, N. (2007) Biological network comparison using graphlet degree distribution. *Bioinformatics*, 23(2), e177-e183.<p>Milenkovic, T. and Przulj, N. (2008) Uncovering Biological Network Function via Graphlet Degree Signatures. *Cancer Informatics*, 6, 257-273.<p>Also refer to the [mfinder home page](http://www.weizmann.ac.il/mcb/UriAlon/groupNetworkMotifSW.html) for information on motif finding and a description of its output file format.