A firm understanding of phylogenetic relationships is central to elucidating many evolutionary questions. However, assessing relationships in many groups requires the compilation and phylogenetic analysis of data sets of molecular and nonmolecular traits for numerous taxa. This is particularly true for many large groups of organisms (such as fungi, bacteria, insects, and green plants) for which relationships have remained obscure despite decades of study using traditional methods. The need for phylogenetic analysis of large data sets is not restricted to higher taxonomic groups, but may involve any portion of the taxonomic hierarchy, extending to the population level, or even to the level of strains of bacteria or viruses.