QuickJoin 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.
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T. Mailund and C.N.S. Pedersen,
QuickJoin—Fast Neighbour-Joining Tree Reconstruction
Bioinformatics, Vol. 20, No. 17, pp 3261-3262, 2004.
T. Mailund, G.S. Brodal, R. Fagerberg, C.N.S. Pedersen, and D. Phillips,
Recrafting the Neighbor-Joining Method
BMC Bioinformatics 2006, 7:29.