UFBoot2: Improving the Ultrafast Bootstrap Approximation

被引：6873

作者：

Diep Thi Hoang ^{[1
]}

Chernomor, Olga ^{[2
]}

von Haeseler, Arndt ^{[2
,3
]}

Minh, Bui Quang ^{[2
]}

Le Sy Vinh ^{[1
]}

机构：

[1] Vietnam Natl Univ, Univ Engn & Technol, Fac Informat Technol, Hanoi, Vietnam

[2] Univ Vienna, Med Univ Vienna, Ctr Integrat Bioinformat Vienna, Max F Perutz Labs, Vienna, Austria

[3] Univ Vienna, Bioinformat & Computat Biol, Fac Comp Sci, Vienna, Austria

来源：

MOLECULAR BIOLOGY AND EVOLUTION | 2018年 / 35卷 / 02期

基金：

奥地利科学基金会;

关键词：

phylogenetic inference; ultrafast bootstrap; maximum likelihood; model violation; polytomies; MAXIMUM-LIKELIHOOD PHYLOGENIES; TREE-SPACE; MODELS; TIME; SUBSTITUTION; CONFIDENCE; ALGORITHM; EVOLUTION; PROTEIN; GENES;

D O I：

10.1093/molbev/msx281

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：518 / 522

页数：5

共 31 条

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