RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
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DOI：
10.1093/bioinformatics/bti191
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发表时间：
2005-02-15
期刊：
影响因子：
5.8
通讯作者：
Meier, H
中科院分区：
文献类型：
--
作者：
Stamatakis, A;Ludwig, T;Meier, H
动机：使用诸如最大似然或贝叶斯推理等统计模型计算大型系统发育树的计算是非常密集的。已经多次证明，这些模型能够比不那么复杂的方法（如简约或邻居连接）更频繁地恢复真树或拓扑上更接近真树的树。由于组合和计算的复杂性，在生物学家的PC工作站在合理的时间内可以计算的树的大小被限制在包含大约100个分类群的树。结果：在本文中，我们介绍了我们的程序RAxML-III的最新版本，用于快速基于最大似然的大型进化树推断，该程序允许在单个PC处理器上在不到24小时内计算1000个分类单元树。我们将RAxML-III与目前最快的最大似然和贝叶斯推理实现（PHYML和MrBayes）进行比较。尽管RAxML-III在合成数据上的表现不如PHYML和MrBayes，但在速度和最终似然值方面，它在所有实际数据对齐上的表现明显优于这两个程序。
Motivation: The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods such as parsimony or neighbor joining. Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist's PC workstation within reasonable time is limited to trees containing approximately 100 taxa.Results: In this paper we present the latest release of our program RAxML-III for rapid maximum likelihood-based inference of large evolutionary trees which allows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor. We compare RAxML-III to the currently fastest implementations for maximum likelihood and bayesian inference: PHYML and MrBayes. Whereas RAxML-III performs worse than PHYML and MrBayes on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values.