An experimental study of Quartets MaxCut and other supertree methods
| dc.creator | Swenson, M. Shel | en |
| dc.creator | Suri, Rahul | en |
| dc.creator | Linder, C. Randal | en |
| dc.creator | Warnow, Tandy | en |
| dc.date.accessioned | 2014-12-15T17:09:54Z | en |
| dc.date.available | 2014-12-15T17:09:54Z | en |
| dc.date.issued | 2011-04-19 | en |
| dc.description | M. Shel Swenson, Rahul Suri, and Tandy Warnow are with the Department of Computer Science, The University of Texas at Austin, Austin TX, USA -- C. Randal Linder is with the Section of Integrative Biology, The University of Texas at Austin, Austin TX, USA | en |
| dc.description.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. | en |
| dc.description.catalogingnote | mswenson@cs.utexas.edu | en |
| dc.description.department | Computer Sciences | en |
| dc.description.department | Integrative Biology | en |
| dc.description.sponsorship | en | |
| dc.identifier.Filename | 1748-7188-6-7 | en |
| dc.identifier.citation | Swenson, M. Shel, Rahul Suri, C. Randal Linder, and Tandy Warnow. “An Experimental Study of Quartets MaxCut and Other Supertree Methods.” Algorithms for Molecular Biology 6, no. 1 (April 19, 2011): 7. doi:10.1186/1748-7188-6-7. | en |
| dc.identifier.doi | doi:10.1186/1748-7188-6-7 | en |
| dc.identifier.uri | http://hdl.handle.net/2152/27804 | en |
| dc.language.iso | English | en |
| dc.publisher | Algorithms for Molecular Biology | en |
| dc.rights | Administrative deposit of works to UT Digital Repository: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access at http://www.biomedcentral.com. The public license is specified as CC-BY: http://creativecommons.org/licenses/by/4.0/. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University. | en |
| dc.subject | Quartets MaxCut | en |
| dc.subject | Supertree methods | en |
| dc.subject | MRP | en |
| dc.title | An experimental study of Quartets MaxCut and other supertree methods | en |
| dc.type | Article | en |
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