Gene function is a subtle concept. The exactness of the relationship between coding sequences and resulting proteins belies the complexity of regulation which genes undergo in the microbial cell. There is, in fact, no reason why two genes of identical coding sequence might not have radically different functions, based solely on differences in their associated regulatory binding sites. This paper is an attempt to discover the sorts of genes that evolve new functions via regulatory change, where genes whose coding sequences remain identical are the limiting case. RegTree is a software tool designed to find such genes by comparing the evolution of homologous groups of genes across several related genomes to the evolution of their regulatory sequences and neighboring genes.
