期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 35, 期 2, 页码 518-522出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msx281
关键词
phylogenetic inference; ultrafast bootstrap; maximum likelihood; model violation; polytomies
资金
- Vietnam National Foundation for Science and Technology Development [102.01-2013.04]
- Austrian Science Fund-FWF [I-2805-B29, I-1824-B22]
- Austrian Science Fund (FWF) [I1824, I2805] Funding Source: Austrian Science Fund (FWF)
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achievingmore unbiased branch supports than SBS undermildmodel violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
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