期刊
BIOINFORMATICS
卷 30, 期 17, 页码 I541-I548出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu462
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资金
- National Science Foundation [0733029, 1062335, 10735191, 1216898]
- University of Alberta, Musea Ventures
- Howard Hughes Medical Institute (HHMI) graduate student fellowship
- Texas Advanced Computing Center (TACC)
- Division Of Environmental Biology
- Direct For Biological Sciences [0733029] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1461364, 1062335] Funding Source: National Science Foundation
- Office of Advanced Cyberinfrastructure (OAC)
- Direct For Computer & Info Scie & Enginr [1216898] Funding Source: National Science Foundation
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.
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