A phylogenetic tree is a tree showing the evolutionary interrelationships among various species or other entities that are believed to have a common ancestor. A phylogenetic tree is a form of a cladogram. In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, and edge lengths correspond to time estimates. Each node in a phylogenetic tree is called a taxonomic unit. Internal nodes are generally referred to as Hypothetical Taxonomic Units (HTUs) as they cannot be directly observed.
A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. Figure 1 depicts a rooted phylogenetic tree, which has been colored according to the three-domain system (Woese 1998).
An unrooted phylogenetic tree is, loosely speaking, a tree derived from a rooted phylogenetic tree by omitting the root. More precisely, it is a forest of rooted phylogenetic trees depicted so that the roots are all linked. Figure 2 depicts an unrooted phylogenetic tree¹ for myosin, a superfamily of proteins. Links to other pictures are given in the Pictures on the Web subsection below.
There are three main methods of constructing phylogenetic trees: Distance based methods such as Neighbour Joining, Parsimony based methods such as Maximum Parsimony , and character based methods such as Maximum Likelihood or Bayesian inference.