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Related Experiment Video

Updated: May 14, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Ultrafast approximation for phylogenetic bootstrap.

Bui Quang Minh¹, Minh Anh Thi Nguyen, Arndt von Haeseler

¹Center for Integrative Bioinformatics Vienna, Max F Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria. minh.bui@univie.ac.at

Molecular Biology and Evolution

|February 19, 2013

Summary

This summary is machine-generated.

Ultrafast bootstrap approximation (UFBoot) accelerates phylogenetic tree analysis by combining resampling with candidate tree selection. This method provides robust and unbiased clade support, improving computational efficiency for large datasets.

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Area of Science:

Computational Biology
Phylogenetics
Bioinformatics

Background:

Nonparametric bootstrap is crucial for assessing phylogenetic tree clade support but computationally intensive.
Growing data volumes exacerbate the computational bottleneck in traditional bootstrap methods.
Existing approximation methods like RAxML rapid bootstrap (RBS) aim to improve speed.

Purpose of the Study:

To introduce an ultrafast bootstrap approximation (UFBoot) for efficient clade support assessment in maximum likelihood phylogenetics.
To develop a computational approach that significantly reduces the time required for bootstrap analysis.
To provide a robust and accurate alternative to standard bootstrap methods for large-scale phylogenetic studies.

Main Methods:

Developed UFBoot by integrating the resampling estimated log-likelihood method with an optimized candidate tree collection strategy.
Implemented a novel stopping rule to automatically determine convergence of branch support values.
Combined UFBoot analysis with maximum likelihood (ML) tree inference.

Main Results:

UFBoot demonstrated a median speed-up of 3.1x for DNA and 10.2x for amino acid alignments compared to RAxML RBS.
Simulations confirmed UFBoot's robustness against moderate phylogenetic model violations.
UFBoot-derived support values were found to be relatively unbiased, offering more direct interpretation than standard bootstrap.

Conclusions:

UFBoot offers a computationally efficient and accurate method for assessing clade support in phylogenetic trees.
The approach provides reliable and less conservative support values, facilitating clearer interpretation.
An accessible software implementation is available for performing UFBoot analysis within ML tree inference workflows.