New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
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DOI：
10.1093/sysbio/syq010
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发表时间：
2010-05-01
影响因子：
6.5
通讯作者：
Gascuel, Olivier
中科院分区：
文献类型：
--
作者：
Guindon, Stephane;Dufayard, Jean-Francois;Gascuel, Olivier
PhyML是一个基于最大似然原理的系统发育软件。早期的PhyML版本使用执行最近邻交换的快速算法来改进合理的起始树拓扑。自最初发表以来(Guindon S.，Gascuel O.2003)。一种简单、快速、准确的最大似然法估计大型系统发育的算法。系统比奥尔。52：696-704)，由于其简单性和在准确性和速度之间的公平折衷，PhyML已被广泛使用(>；2500篇ISI Web of Science中的引文)。与此同时，围绕PhyML的研究仍在继续，本文描述了在该程序中实现的新算法和方法。首先，我们提出了一种新的算法，使用子树剪枝和重新嫁接拓扑移动来搜索具有用户定义强度的树空间。这里使用简约准则来滤除关于似然函数的最不可能的拓扑修改。对不同大小的真实核苷酸和氨基酸数据集的分析表明，该方法具有良好的性能。其次，我们描述了一种新的测试来评估数据对系统发育内部分支的支持。这种方法扩展了最近提出的近似似然比检验，并依赖于一个非参数的Shimodaira-Hasegawa类过程。对真实比对的详细分析揭示了这种新方法与更经典的非参数Bootstrap方法之间的联系。总体而言，我们的测试表明，PhyML的最新版本(3.0)是快速、准确、稳定的，并且可以随时使用。网站服务器和二进制文件可从http://www.atgc-montpellier.fr/phyml/.获得
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (> 2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.