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Background  Chaining is a major problem in constructing gene families.    Results  We define a new kind of cluster on graphs with strong and weak edges: soft cliques with backbones (SCWiB). This differs from other definitions in how it controls the "chaining effect", by ensuring clusters satisfy a tolerant edge density criterion that takes into account cluster size. We implement algorithms for decomposing a graph of similarities into SCWiBs. We compare examples of output from SCWiB and the Markov Cluster Algorithm (MCL), and also compare some curated  Arabidopsis thaliana  gene families with the results of automatic clustering. We apply our method to 44 published angiosperm genomes with annotation, and discover that  Amborella trichopoda  is distinct from all the others in having substantially and systematically smaller proportions of moderate- and large-size gene families.    Conclusions  We offer several possible evolutionary explanations for this result.

Gene families as soft cliques with backbones: Amborellacontrasted with other flowering plants