Figure 1

Performance of our methods using the simple approximation to Q. The plots show the running time of QuickTree, and QuickJoin with the depth-first search (DFS) method and with the priority queue (p.queue) method with and without sampling (see Methods), with the first approximation of Q described in the Methods section. The input for the runs is distance matrices for the Pfam alignments with 200 to 1000 sequences. The depth-first search without sampling performs very poorly and is removed on the plot on the right to better show the performance of the remaining methods.