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.
Mailund et al. BMC Bioinformatics 2006 7:29 doi:10.1186/1471-2105-7-29