Figure 3

Results of three different topology reconstruction methods: NJ , ML and EMtree . Results of the three different topology reconstruction methods NJ (a), ML (b) and EMtree (c) on the tree space proposed by Huelsenbeck (see Figure 2). On the left, data have been generated using a time-homogeneous continuous-time K81 model and the topology is estimated by NJ (with K81 distance), ML (estimating a homogeneous K81 model), and EMtree (on K81*). On the right, data have been generated using time nonhomogeneous continuous-time K81 model and the topology is estimated by NJ (with K81 distance), ML (estimating time nonhomogeneous K81 continuous-time model), and EMtree (on K81*). The alignments considered in this figure have length 600 bp.