TY - GEN
T1 - An experimental study of quartets MaxCut and other supertree methods
AU - Swenson, M. Shel
AU - Suri, Rahul
AU - Linder, C. Randal
AU - Warnow, Tandy
N1 - Funding Information:
We thank Sagi Snir for assistance with using the QMC code and for providing the software for generating the quartet encodings Exp+TSQ, Geo+TSQ, and AllQuartets. This work was supported by the US National Science Foundation ITR-0331453, for the CIPRES project.
PY - 2010
Y1 - 2010
N2 - Although many supertree methods have been developed in the last few decades, none has been shown to produce more accurate trees than the popular Matrix Representation with Parsimony (MRP) method. In this paper, we evaluate the performance of several supertree methods based upon the Quartets MaxCut method of Snir and Rao. We show that two of these methods usually outperform MRP and all other supertree methods we studied under many realistic model conditions. In addition, we show that the popular criterion of minimizing the total topological distance to the source trees is only weakly correlated with topological accuracy, and therefore that evaluating supertree methods on biological datasets is problematic.
AB - Although many supertree methods have been developed in the last few decades, none has been shown to produce more accurate trees than the popular Matrix Representation with Parsimony (MRP) method. In this paper, we evaluate the performance of several supertree methods based upon the Quartets MaxCut method of Snir and Rao. We show that two of these methods usually outperform MRP and all other supertree methods we studied under many realistic model conditions. In addition, we show that the popular criterion of minimizing the total topological distance to the source trees is only weakly correlated with topological accuracy, and therefore that evaluating supertree methods on biological datasets is problematic.
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U2 - 10.1007/978-3-642-15294-8_24
DO - 10.1007/978-3-642-15294-8_24
M3 - Conference contribution
AN - SCOPUS:78049481079
SN - 3642152937
SN - 9783642152931
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 288
EP - 299
BT - Algorithms in Bioinformatics - 10th International Workshop, WABI 2010, Proceedings
T2 - 10th International Workshop on Algorithms in Bioinformatics, WABI 2010
Y2 - 6 September 2010 through 8 September 2010
ER -