Unrooted phylogenies

Since the data for the ancestors are usually missing, the phylogenetic trees produced by PHASE are only schematic trees comprising a set of nodes linked together by branches. Terminal nodes, usually called tips or leaves, are known sequences of existing organisms or contemporary taxa. Internal nodes are bifurcation points between genetically isolated groups.

The analytical techniques used in PHASE result in the inference of an unrooted, strictly bifurcating tree. The location of the common ancestor of all the species under study -- i.e., the earliest point in time -- cannot be identified by our inference method. An unrooted, strictly bifurcating tree can be seen as a kind of network where all the internal nodes are linked to exactly three others nodes, either internal nodes or leaves. To produce a neat tree-like structure, one or more outgroup species, known to be genetically isolated from all the others, should be used to root the tree (see figure 2.1).

Figure 2.1: Two equivalent representations of the same unrooted tree