UFBoot2: Improving the Ultrafast Bootstrap Approximation

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.

Reclassification of Parapterulicium Corner (Pterulaceae, Agaricales), contributions to Lachnocladiaceae and Peniophoraceae (Russulales) and introduction of Baltazaria gen. nov.

“…The best-fit evolutionary models for this analysis were estimated by the built-in ModelFinder (option -m MF+MERGE) allowing the partitions to share the same set of branch lengths but with their own evolution rate (-spp option) (Chernomor et al 2016; Kalyaanamoorthy et al 2017). Branch support was assessed with 1000 replicates of ultrafast bootstrapping (Hoang et al 2018). …”

Phylogeography and Genetic Diversity of Francisella tularensis subsp. holarctica in France (1947–2018)

“…Based on the file of concatenated SNPs generated by iVarCall2, maximum likelihood (ML) phylogenetic trees were created with IQTree (Nguyen et al, 2015), SH-aLRT (Anisimova et al, 2011) and UFBoot2 (Hoang et al, 2018) supports, set to 1000 replicates), after using Modelfinder (Kalyaanamoorthy et al, 2017) to determine the best model (TVM model in this study). The best-scoring ML tree was graphically represented with iTOL viewer (Supplementary Figure S1) (Letunic and Bork, 2016) and compared with the canSNP nomenclature to detect new subclades.…”

All Eukaryotes Are Sexual, unless Proven Otherwise

“…Resulting alignments were trimmed with Trimal and used as input for Iqtree reconstructions . Reconstructions were performed with Iqtree setting a simple mixed substitution model (LG + C10 + F + G) arbitrarily selected and 1000 Ultrafast bootstraps . The resulting trees were employed for the discrimination of possible meiotic paralogues for each eukaryotic groupings or arbitrary selections of putative asexuals that received more attention.…”