ABSTRACT
Functional genomics refers to studying the function of genes on a genome-wide scale. Prior to the generation of whole genome sequences, function was studied on a gene-by-gene or protein-by-protein basis. With the availability of whole genome sequences, functional studies have started to include larger numbers of genes, and a new dimension has been added. This new dimension involves the interaction of genes to produce phenotypes, anatomical trends, behavioral trends, and other kinds of evolutionary phenomena. Knowing the phylogeny of organisms when doing functional studies allows us to order evolutionary events and hence reconstruct the evolutionary history of the events involved in the overall function of genes and proteins. The scale of analysis in these studies is very different from most phylogenetic studies and requires that data not only be managed for the various taxa in a study but also for the various nodes in a phylogenetic tree that hypothesizes the relationships of the taxa.
