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UltrafastApproximation forPhylogeneticBootstrap Bùi Quang MinhMinh Anh NguyenA. von Haeseler2013 год

Ultrafast Approximation for Phylogenetic Bootstrap
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Аннотация: Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and the Shimodaira–Hasegawa-like approximate likelihood ratio test have been introduced to speed up the bootstrap. Here, we suggest an ultrafast bootstrap approximation approach (UFBoot) to compute the support of phylogenetic groups in maximum likelihood (ML) based trees. To achieve this, we combine the resampling estimated log-likelihood method with a simple but effective collection scheme of candidate trees. We also propose a stopping rule that assesses the convergence of branch support values to automatically determine when to stop collecting candidate trees. UFBoot achieves a median speed up of 3.1 (range: 0.66–33.3) to 10.2 (range: 1.32–41.4) compared with RAxML RBS for real DNA and amino acid alignments, respectively. Moreover, our extensive simulations show that UFBoot is robust against moderate model violations and the support values obtained appear to be relatively unbiased compared with the conservative standard bootstrap. This provides a more direct interpretation of the bootstrap support. We offer an efficient and easy-to-use software (available at http://www.cibiv.at/software/iqtree) to perform the UFBoot analysis with ML tree inference.
Год издания: 2013
Авторы: Bùi Quang Minh, Minh Anh Nguyen, A. von Haeseler
Издательство: Oxford University Press
Источник: Molecular Biology and Evolution
Ключевые слова: Genomics and Phylogenetic Studies, Evolution and Paleontology Studies, Genetic diversity and population structure
Другие ссылки: Molecular Biology and Evolution (HTML)
University of Groningen research database (University of Groningen / Centre for Information Technology) (HTML)
Data Archiving and Networked Services (DANS) (PDF)
Data Archiving and Networked Services (DANS) (HTML)
Europe PMC (PubMed Central) (HTML)
PubMed Central (HTML)
PubMed (HTML)