Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon. Taxa can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

Typically, phylogeny is represented by a tree. Each taxon of interest is depicted at the tip of the branch, and the branches represent the relationship between these taxa. Closely related taxa share a larger portion of their genome, resulting in morphological similarities. Sister taxa share an immediate common ancestor, represented by a shared node.

Nodes in the tree depict a morphological characteristic or molecular change that differentiates taxa. All taxa that directly connect to a specific node share a recent common ancestor. Hence, the root of the tree is the ancestor shared by all taxa in the tree. A tree without a root represents the relationship of taxa but does not provide information on the shared common ancestor.

The length of the branches of a tree may or may not have a meaning. In a scaled tree, the length of the branch may either represent time or the number of changes that occurred since the taxa evolved from a common ancestor.