Progressive Multiple Alignment of Protein Sequences and the Construction of Phylogenetic Trees

Early attempts to use quantitative measures to provide information on divergent evolution of macromolecules include estimates, such as the degree of crossreactivity of antisera to purified proteins (1 ,2 ), the degree of interspecific hybridization of DNA (3 ), and differences in peptide profile of digested proteins (4 ,5 ). The inventions of modern nucleic acid and protein sequencing techniques have led to an avalanche of protein sequence data, which provide a more extensive and quantitative tool for exploration of evolutionary relationships than the aforementioned biological characteristics. Grouping of proteins into families or superfamilies and the reconstruction of protein or organismic history from extant protein sequences can be portrayed in the form of an evolutionary tree. The branching order of such a tree identifies the points of divergence for proteins or organisms that share a common ancestry, whereas the branch lengths reflect the evolutionary distances between present-day proteins and proteins that existed at the point of divergence.