UFBoot2: Improving the Ultrafast Bootstrap Approximation

TLDR

The standard bootstrap (SBS) is widely used in maximum likelihood phylogenetic analyses despite its computational intensity. The study develops UFBoot2, an accelerated ultrafast bootstrap method that reduces overestimation of branch supports under polytomies or severe model violations. UFBoot2 is implemented in IQ‑TREE v1.6, offers faster resampling strategies for phylogenomic data, and mitigates overestimation of branch supports under polytomies or severe model violations. UFBoot2 achieves median speedups of 778× over SBS and 8.4× over RAxML rapid bootstrap, and UFBoot has already been widely adopted as an efficient alternative to SBS.

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.