The maximal cliques represent a clustering of the sequences detected with BLAST. Thus with the help of this clique-finding algorithm, clusters can now be quickly and automatically identified even from very large BLAST reports. The result of the clustering can then be further processed for example for phylogenetic reconstructions of the sequences in the clusters. At this point one might discuss the biological usefulness to compute all maximal cliques. As we have seen from the biological data sets used for our experiments, it is very common to have largely interlinked sequences, i.e., where one unique clustering and/or maximal clique does not exist. This is for example a common feature in the case of multidomain proteins, where the query protein contains say k domains, and BLAST reported subject proteins will show a variety of combinations of these k domains. A goal of applying the maximal cliques search algorithm is to cluster individual domains as well as all possible combinations of domains. The examples in figure 14 illustrate the result of these clusterings. Here one also clearly sees that other reasonable partitions are possible.