TribeMCL

Stijn van Dongen's Markov Cluster Algorithm package available here. This package provides tools for cluster gene families from sequence similarity searches like BLAST or FASTA [1].

References

1. Enright AJ, Van Dongen S, and Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002 Apr 1;30(7):1575-84.