1. Introduction
Phylogenetic trees are used to represent the evolutionary history of a set of organisms (also called taxa). A multiple alignment of a small region of their DNA or protein sequences can be used as input for the computation of phylogenies. In a computational context phylogenetic trees are usually strictly bifurcating unrooted trees. The organisms of the alignment are located at the tips and the inner nodes represent extinct common ancestors. The branches of the tree represent the time which was required for the mutation of one species into another-new-one. The inference of phylogenies with computational methods has many important applications in medical and biological research, such as e.g. drug discovery and conservation biology (see [1] for a summary). Due to the rapid growth of available sequence data and the constant improvement of multiple alignment methods it has now become feasible to compute large trees which comprise more than 1,000 organisms. The computation of the tree-of-life containing representatives of all living beings on earth is one of the grand challenges in Bioinformatics.