UFBoot2: Improving the Ultrafast Bootstrap Approximation

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 and 8.4 times (median) faster than SBS and RAxML rapid bootstrap on tested datasets, respectively. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.

• Publication year

  2017

• Venue

  bioRxiv

• Publication date

  2017-06-22

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/molbev/msx281PMID 29077904PMCID 5850222
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Supplementary Data: Ufboot2: Improving The Ultrafast Bootstrap Approximation

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