期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 35, 期 2, 页码 486-503出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msx302
关键词
molecular evolution; tree space; topology; heuristic search
资金
- National Science Foundation [DEB-1442113, DEB-1442148]
- DOE Great Lakes Bioenergy Research Center (DOE Office of Science) [BER DE-FC02-07ER64494]
- USDA National Institute of Food and Agriculture (Hatch project) [1003258]
- National Key Project for Basic Research of China (973 Program) [2015CB150600]
- Pew Charitable Trusts
- NIFA [1003258, 690581] Funding Source: Federal RePORTER
- Direct For Biological Sciences
- Division Of Environmental Biology [1442148] Funding Source: National Science Foundation
The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popularmaximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets with hundreds to thousands of genes and up to 200 taxa with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that themore exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation-based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the programs' relative performance. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of largescale phylogenomic data analyses.
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