Example of BranchClust selection steps for a superfamily tree for 5 different taxa with 3 clusters. Figure 5A. Unrooted original tree. Figure 5B. Tree is initially rooted inside the cluster. The ancestor of the most distant leaf from the root is set to be root 1. Figure 5C. Tree is re-rooted with the root 1. The ancestor of the most distant leaf from the root 1 is set to be root 2. Selection starts from the most distant from the root 1 leaf and ends when it encounters branch containing MANY (here 4) species. First cluster is selected and removed from the tree. The node is marked with a leaf "R". Figure 5D. Tree is re-rooted with the root 2. Figure 5E. Tree is re-rooted at the ancestor of the selected cluster and the selection continues. Figure 5F. Cluster 2 is selected, removed from the tree, the node of cut is marked with a leaf "R". Figure 5G. Tree is not re-rooted because the ancestor of the removed cluster is already the root. Selection continues. The last cluster is selected. End of selection.