Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm

Quartet-based phylogeny reconstruction methods, such as Quartet Puzzling, were introduced in the hope that they might be competitive with maximum likelihood methods, without being as computationally intensive. However, despite the numerous quartet-based methods that have been developed, their performance in simulation has been disappointing. In particular, Ranwez and Gascuel, the developers of one of the best quartet methods, conjecture that quartet-based methods have inherent limitations that make them unable to produce trees as accurate as neighbor joining or maximum parsimony. In this paper, we present Short Quartet Puzzling, a new quartet-based phylogeny reconstruction algorithm, and we demonstrate the improved topological accuracy of the new method over maximum parsimony and neighbor joining, disproving the conjecture of Ranwez and Gascuel. We also show a dramatic improvement over Quartet Puzzling. Thus, while our new method is not compared to any ML method (as it is not expected...

• Type: Journal
• Year: 2008
• Where: JCB
• Authors: Sagi Snir, Tandy Warnow, Satish Rao
• Keywords: JCB 2008, Quartet Puzzling, Quartet-based Methods, Quartet-based Phylogeny Reconstruction