You do the clustering, we tell you how good it is.

 
Gibbons, F.D. and Roth F.P., (2002)
Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation. 
Genome Research, vol. 12, pp1574-1581.

This is not a new clustering algorithm. Rather, it is a way to judge the quality of data that have been clustered elsewhere. We do this by evaluating the mutual information between a gene's membership in a cluster, and the attributes it possesses, as annotated by the Saccharomyces Genome Database (SGD) You can upload several files of clustered data at once and compare them.

• The Gene Ontology has grown considerably. In addition, growth has not affected the three branches (Biological Process, Cellular Component, Molecular Function) equally. While this does not invalidate the results produced by ClusterJudge, it will no reflect the current level of functional annotation. If this is important to you, you may wish to download ClusterJudge's source code, and use it to score your clusters with an updated version of the Gene Ontology.
• ClusterJudge works only for Saccharomyces cerevisiae (brewer's/baker's/budding yeast). Over time, as annotation improves, ORFs may become obsolete, and new ORFs may be introduced. Such changes in a single ORF are unlikely to substantially change the scores produced by ClusterJudge, thought the effects will accumulate over time.