tailieunhanh - Báo cáo sinh học: "An experimental study of Quartets MaxCut and other supertree method"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: An experimental study of Quartets MaxCut and other supertree methods. | Swenson et al. Algorithms for Molecular Biology 2011 6 7 http content 6 1 7 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access An experimental study of Quartets MaxCut and other supertree methods M Shel Swenson1 Rahul Suri1 C Randal Linder2 and Tandy Warnow1 Abstract Background Supertree methods represent one of the major ways by which the Tree of Life can be estimated but despite many recent algorithmic innovations matrix representation with parsimony MRP remains the main algorithmic supertree method. Results We evaluated the performance of several supertree methods based upon the Quartets MaxCut QMC method of Snir and Rao and showed that two of these methods usually outperform MRP and five other supertree methods that we studied under many realistic model conditions. However the QMC-based methods have scalability issues that may limit their utility on large datasets. We also observed that taxon sampling impacted supertree accuracy with poor results obtained when all of the source trees were only sparsely sampled. Finally we showed that the popular optimality criterion of minimizing the total topological distance of the supertree to the source trees is only weakly correlated with supertree topological accuracy. Therefore evaluating supertree methods on biological datasets is problematic. Conclusions Our results show that supertree methods that improve upon MRP are possible and that an effort should be made to produce scalable and robust implementations of the most accurate supertree methods. Also because topological accuracy depends upon taxon sampling strategies attempts to construct very large phylogenetic trees using supertree methods should consider the selection of source tree datasets as well as supertree methods. Finally since supertree topological error is only weakly correlated with the supertree s topological distance to its source trees development and testing of supertree methods presents methodological challenges. Background .