UFBoot2: Improving the Ultrafast Bootstrap Approximation

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 viol...

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Bibliographic Details
Published inMolecular biology and evolution Vol. 35; no. 2; pp. 518 - 522
Main Authors Hoang, Diep Thi, Chernomor, Olga, von Haeseler, Arndt, Minh, Bui Quang, Vinh, Le Sy
Format Journal Article
LanguageEnglish
Published United States Oxford University Press 01.02.2018
Subjects
Approximation
Computing time
Likelihood Functions
Models, Genetic
Phylogeny
Resampling
Resources
Risk reduction
Software
polytomies
model violation
phylogenetic inference
ultrafast bootstrap
maximum likelihood
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Summary: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 http://www.iqtree.org.
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These authors contributed equally to this work.
Associate editor: Michael S. Rosenberg
ISSN:0737-4038
1537-1719
1537-1719
DOI:10.1093/molbev/msx281