Article

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi HoangFaculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, VietnamOlga ChernomorCenter for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, AustriaArndt von HaeselerBioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, AustriaBùi Quang MinhCenter for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, AustriaLê Sỹ VinhFaculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam

2017en

ABI

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 http://www.iqtree.org.

Identifiers

DOI: 10.1093/molbev/msx281

Citations and references

Cited by 90 references

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