Using all-pairs or all-pairs-max clearly require Θ(n 4 k) time to build the distance matrix and using the default O(n 3) neighbor joining algorithm  would result in Θ(n 4 k) total running time. The running times of tree-sum and distance-sum depend on the selection of anchors, and also the exact distance method and supertree method used. Building each double anchored distance matrix requires Θ(n 2 k); thus, building m matrices requires Θ(n 2 m k). Using a fast neighbor joining algorithm (e.g., FNJ , or NINJA ), the running time of distance method can be O(n 2).