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UFBoot2: Improving the Ultrafast Bootstrap Approximation

Hoang, Thi Diep and Chernomor, Olga and Arndt, von Haeseler and Bui, Quang Minh and Le, Sy Vinh (2018) UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular Biology and Evolution, 35 (2). pp. 518-522. ISSN 0737-4038

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Abstract 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 achieving more unbiased branch supports than SBS under mild model 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

Item Type: Article
Subjects: Information Technology (IT)
Scopus-indexed journals
ISI-indexed journals
Divisions: Faculty of Information Technology (FIT)
Depositing User: Ms. Diep/T Hoang
Date Deposited: 03 Jun 2019 04:14
Last Modified: 03 Jun 2019 04:14

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