UFBoot2: Improving the ultrafast bootstrap approximation

Diep Thi Hoang; Olga Chernomor; Arndt Von Haeseler; Bui Quang Minh; Le Sy Vinh

doi:10.1093/molbev/msx281

UFBoot2: Improving the ultrafast bootstrap approximation

Diep Thi Hoang, Olga Chernomor, Arndt Von Haeseler, Bui Quang Minh, Le Sy Vinh^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

5488 Citations (Scopus)

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 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.

Original language	English
Pages (from-to)	518-522
Number of pages	5
Journal	Molecular Biology and Evolution
Volume	35
Issue number	2
DOIs	https://doi.org/10.1093/molbev/msx281
Publication status	Published - Feb 2018
Externally published	Yes

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title = "UFBoot2: Improving the ultrafast bootstrap approximation",

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 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.",

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author = "Hoang, {Diep Thi} and Olga Chernomor and {Von Haeseler}, Arndt and Minh, {Bui Quang} and Vinh, {Le Sy}",

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AU - Chernomor, Olga

AU - Von Haeseler, Arndt

AU - Minh, Bui Quang

AU - Vinh, Le Sy

N1 - Publisher Copyright: © The Author 2017.

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AB - 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.

KW - maximum likelihood

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UFBoot2: Improving the ultrafast bootstrap approximation

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