TY  - JOUR
ID  - SisLab3437
UR  - https://dx.doi.org/10.1093/molbev/msx281
IS  - 2
A1  - Hoang, Thi Diep
A1  - Chernomor, Olga
A1  - Arndt, von Haeseler
A1  - Bui, Quang Minh
A1  - Le, Sy Vinh
Y1  - 2018/02/01/
N2  - 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.
PB  - Oxford University Press
JF  - Molecular Biology and Evolution
VL  - 35
SN  - 0737-4038
TI  - UFBoot2: Improving the Ultrafast Bootstrap Approximation
SP  - 518
AV  - public
EP  - 522
ER  -