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RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

机译：RAxML-III：一种用于大型系统树的基于最大似然性推断的快速程序

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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. Availability SUPPLEMENTARY INFORMATION: RAxML-III including all alignments and final trees mentioned in this paper is freely available as open source code at http://wwwbode.cs.tum/~stamatak CONTACT: stamatak@cs.tum.edu.
机译：动机：使用统计模型（例如最大似然或贝叶斯推断）来计算大型系统树的计算量非常大。反复证明，这些模型能够比不那么复杂的方法（例如简约或邻居加入）更频繁地恢复真实树或在拓扑上更接近真实树的树。由于组合和计算的复杂性，在生物学家的PC工作站上可以在合理时间内计算出的树木的大小仅限于包含大约100个分类单元的树木。结果：在本文中，我们提出了最新版本的RAxML-III程序，用于大型进化树的基于快速最大似然性的推断，它允许在单个PC处理器上在不到24小时的时间内计算1.000个分类单元树。我们将RAxML-III与目前最快的实现方案进行了比较，以求最大似然和贝叶斯推断：PHYML和MrBayes。尽管RAxML-III在合成数据上的性能比PHYML和MrBayes差，但在速度和最终似然值方面，在所有实际数据比对方面，其性能明显优于两个程序。可用性补充信息：本文中提到的RAxML-III（包括所有比对和最终树）可作为开放源代码免费获得，网址为http：//wwwbode.cs.tum/~stamatak。联系人：stamatak@cs.tum.edu。

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