Short Quartet Puzzling: A new quartet-based phylogeny reconstruction algorithm

Sagi Snir, Tandy Warnow, Satish Rao

Research output: Contribution to journalArticlepeer-review


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 to be as accurate as the best of these), this study shows that quartet methods are not as limited in performance as was previously conjectured, and opens the possibility to further improvements through new algorithmic designs.

Original languageEnglish
Pages (from-to)91-103
Number of pages13
JournalJournal of Computational Biology
Issue number1
StatePublished - 1 Jan 2008
Externally publishedYes


  • Algorithms
  • Biology
  • Computational molecular biology
  • Evolution

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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