Format

Send to

Choose Destination
Mol Biol Evol. 2018 Feb 1;35(2):518-522. doi: 10.1093/molbev/msx281.

UFBoot2: Improving the Ultrafast Bootstrap Approximation.

Author information

1
Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam.
2
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria.
3
Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.

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.

KEYWORDS:

maximum likelihood; model violation; phylogenetic inference; polytomies; ultrafast bootstrap

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center