“UFBoot2: Improving the Ultrafast Bootstrap Approximation” (2017), by Diep Thi Hoang et al. Genetics and Biochemistry research paper. Original abstract below, unchanged. A free PDF is available.

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler et al. · October 24, 2017 · Genetics and Biochemistry

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.

Free PDF DOI: 10.1093/molbev/msx281