Brinkmeyer Malte, Griebel Thasso, Böcker Sebastian
Department of Computer Science, Friedrich Schiller University, 07743 Jena, Germany.
Adv Bioinformatics. 2011;2011:524182. doi: 10.1155/2011/524182. Epub 2011 Dec 21.
Supertree methods allow to reconstruct large phylogenetic trees by combining smaller trees with overlapping leaf sets into one, more comprehensive supertree. The most commonly used supertree method, matrix representation with parsimony (MRP), produces accurate supertrees but is rather slow due to the underlying hard optimization problem. In this paper, we present an extensive simulation study comparing the performance of MRP and the polynomial supertree methods MinCut Supertree, Modified MinCut Supertree, Build-with-distances, PhySIC, PhySIC_IST, and super distance matrix. We consider both quality and resolution of the reconstructed supertrees. Our findings illustrate the tradeoff between accuracy and running time in supertree construction, as well as the pros and cons of voting- and veto-based supertree approaches. Based on our results, we make some general suggestions for supertree methods yet to come.
超树方法允许通过将具有重叠叶集的较小树合并为一个更全面的超树来重建大型系统发育树。最常用的超树方法，即简约矩阵表示法（MRP），能生成准确的超树，但由于其潜在的硬优化问题，速度相当慢。在本文中，我们进行了一项广泛的模拟研究，比较了MRP与多项式超树方法MinCut Supertree、Modified MinCut Supertree、Build-with-distances、PhySIC、PhySIC_IST和超距离矩阵的性能。我们考虑了重建超树的质量和分辨率。我们的研究结果说明了超树构建中准确性和运行时间之间的权衡，以及基于投票和否决的超树方法的优缺点。基于我们的结果，我们对未来的超树方法提出了一些一般性建议。
