ASTRAL: genome-scale coalescent-based species tree estimation.
ASTRAL: genome-scale coalescent-based species tree estimation.
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DOI：
10.1093/bioinformatics/btu462
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发表时间：
2014-09-01
期刊：
影响因子：
--
通讯作者：
Warnow T
中科院分区：
文献类型：
--
作者：
Mirarab S;Reaz R;Bayzid MS;Zimmermann T;Swenson MS;Warnow T
动机：物种树为基础生物学提供了深入见解，包括进化机制以及它如何改变生物分子的功能和结构、生物多样性以及基因与物种之间的共同进化。然而，基因树常常与物种树不同，这给物种树的估计带来了挑战。基因树和物种树之间拓扑结构冲突的最常见原因之一是不完全谱系分选（ILS），它由多物种溯祖模型模拟。虽然已经开发了许多从多个基因估计物种树的方法，其中一些在多物种溯祖模型下有统计保证，但现有方法对于基因组规模的分析计算强度太大，或者在一些现实条件下已被证明准确性较差。
结果：我们提出了ASTRAL，一种从多个基因估计物种树的快速方法。ASTRAL在统计上是一致的，可以在包含数千个基因的数据集上运行，并且具有出色的准确性——比MP - EST和BUCKy的群体树（两种基于溯祖的具有统计一致性的主要方法）更优。除了ILS水平较低或基因树太少的情况外，ASTRAL通常比使用最大似然法的串联更准确。
可用性和实现：ASTRAL以开源形式在https://github.com/smirarab/ASTRAL/提供。本文研究的数据集可在http://www.cs.utexas.edu/users/phylo/datasets/astral获取。
联系：warnow@illinois.edu
补充信息：补充数据可在Bioinformatics在线获取。
Motivation: Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions. Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees. Availability and implementation: ASTRAL is available in open source form at https://github.com/smirarab/ASTRAL/. Datasets studied in this article are available at http://www.cs.utexas.edu/users/phylo/datasets/astral. Contact: warnow@illinois.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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