Phylogenetic trees take several forms: They can be rooted or unrooted, binary or general, and may show, or not show, edge lengths. A rooted tree is a tree in which one of the nodes is stipulated to be the root, and thus the direction of ancestral relationships is determined. An unrooted tree, as could be imagined, has no pre-determined root and therefore induces no hierarchy. Therefore, in this case, the distance between the nodes should be symmetric (since the tree edges are not directed). Rooting an unrooted tree involves inserting a new node, which will function as the root node. This can be done by introducing an outgroup, a species that is definitely distant from all the species of interest. The proposed root will be the direct predecessor of the outgroup. Figures 8.1 and 8.2 show a rooted tree and its unrooted counterpart, respectively.
A binary, or bifurcating, tree is of course a tree in which a node may have only 0 to 2 subnodes, that is, in an unrooted tree, up to three neighbors. It is sometimes useful to allow more than 2 subnodes (multifurcation), but the discussion in this lecture will be limited to binary trees.
A tree can show edge lengths, indicating the genetic distance between the connected nodes. We sometimes assume the existence of a molecular clock, a constant pace of the evolutionary processes. If this is the case, we could theoretically produce a phylogenetic distance-preserving tree which can be presented along a time-axis - assigning to each node the time in which it ``occurred'' in the history of evolution. In such a ``perfect'' tree, the length of each edge would be the difference in time between the parent node and the child node.
There are two types of data used for building phylogenetic trees: