eprintid: 3437
rev_number: 9
eprint_status: archive
userid: 282
dir: disk0/00/00/34/37
datestamp: 2019-06-03 04:14:06
lastmod: 2019-06-03 04:14:06
status_changed: 2019-06-03 04:14:06
type: article
metadata_visibility: show
creators_name: Hoang, Thi Diep
creators_name: Chernomor, Olga
creators_name: Arndt, von Haeseler
creators_name: Bui, Quang Minh
creators_name: Le, Sy Vinh
creators_id: diepht@vnu.edu.vn
creators_id: vinhls@vnu.edu.vn
title: UFBoot2: Improving the Ultrafast Bootstrap Approximation
ispublished: pub
subjects: IT
subjects: Scopus
subjects: isi
divisions: fac_fit
abstract: 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.
date: 2018-02-01
date_type: published
publisher: Oxford University Press
official_url: https://dx.doi.org/10.1093/molbev/msx281
id_number: 10.1093/molbev/msx281
full_text_status: public
publication: Molecular Biology and Evolution
volume: 35
number: 2
pagerange: 518-522
refereed: TRUE
issn: 0737-4038
related_url_url: https://academic.oup.com/mbe
related_url_type: pub
citation:   Hoang, Thi Diep and Chernomor, Olga and Arndt, von Haeseler and Bui, Quang Minh and Le, Sy Vinh  (2018) UFBoot2: Improving the Ultrafast Bootstrap Approximation.  Molecular Biology and Evolution, 35  (2).   pp. 518-522.  ISSN 0737-4038     
document_url: https://eprints.uet.vnu.edu.vn/eprints/id/eprint/3437/1/MinhChung_CongTrinh1.pdf