Quick-Join implements a heuristic for speeding up neighbour joining, making neighbour joining feasible for large sets of taxa. The inferred tree is identical to the tree inferred by the traditional neighbour joining method, but the heuristic will (potentially) construct the tree significantly faster. License: GNU General Public License (GPL) Changes:
This version splits the output, when doing bootstrapping, into two trees, one annotated with branch lengths and one annotated with bootstrap values. This makes post-processing easier, since most tools support a single branch annotation but not two.