The study of sequence space, and the deciphering of the structure of protein families and subfamilies, has up to now been required for work in comparative genomics and for the prediction of protein function. With the emergence of structural proteomics projects, it is becoming increasingly important to be able to select protein targets for structural studies that will appropriately cover the space of protein sequences, functions and genomic distribution. These problems are the motivation for the development of methods for clustering protein sequences and building families of potentially orthologous sequences, such as those proposed here.