Reconstructing phylogenies from noisy quartets in polynomial time with a high success probability

Background: In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is measured by simulations on synthetic datasets with known "true" phylogenies, while little theoretical analysis has been done. In this paper, we present a new model-based approach to measuring the accuracy of a quartet-based phylogeny reconstruction method. Under this model, we propose three efficient algorithms to reconstruct the "true" phylogeny with a high success probability. Results: The first algorithm can reconstruct the "true" phylogeny from the input quartet topology set without quartet errors in O(n2) time by querying at most (n - 4) log(n - 1) quartet topologies, where n is the number of the taxa. When the input quartet topology set contains errors, the second algorithm can reconstruct the "true" phylogeny with a prob...

• Type: Journal
• Year: 2008
• Where: ALMOB
• Authors: Gang Wu, Ming-Yang Kao, Guohui Lin, Jia-Huai You
• Keywords: Algorithm, ALMOB 2008, Phylogeny Reconstruction Methods, Quartet-based Phylogeny Reconstruction