IQPNNI (Important Quartet Puzzling and NNI Operation) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a list of potential candidate trees. The key ingredient is the definition of so-called important quartets (IQs), which allow the computation of an intermediate tree in O(n^2) time for n sequences. The resulting tree is then further optimized by applying the nearest neighbor interchange (NNI) operation. Subsequently a random fraction of the sequences is deleted from the best tree found so far. The deleted sequences are then re-inserted in the smaller tree using the important quartet puzzling (IQP) algorithm.
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Le Sy Vinh and Arndt von Haeseler (2004)
IQPNNI: Moving fast through tree space and stopping in time.
Mol. Biol. Evol., 21(8):1565-1571.