How Many Bootstrap Replicates Are Necessary?

By Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis. Annual International Conference on Research in Computational Molecular Biology, 2009

1,214 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/553ee5b2a8982c8113d8c1cee4abaf6d6e8cfc81

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Citations in the corpus

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, methodology): “For each analysis, branch support was estimated using the automatic bootstrap convergence function that calculates a stopping rule to determine when enough replicates have been generated (Pattengale et al. 2010).”
Evolutionary History of the Hymenoptera. (2017, methodology): “Node support was inferred with the bootstrap method [35].”
The sooty moulds (2014, methodology): “The number of replicates was automatically inferred using the stopping criterion (Pattengale et al. 2009).”
Ultrafast Approximation for Phylogenetic Bootstrap (2013, methodology): “Similar ideas have been employed in the bootstopping criterion (Pattengale et al. 2010).”
Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element (2014, methodology): “The number of bootstrap pseudoreplicates over which node support is not expected to be significantly altered was evaluated using the frequency-based and majority-rule bootstopping criteria (Pattengale et al., 2010).”
MEGA12: Molecular Evolutionary Genetic Analysis Version 12 for Adaptive and Green Computing (2024, neutral): “Users frequently choose to generate a large number of re-sampled MSAs (500 to 2,000 replicates) because every BS value is an estimate whose accuracy is determined by the number of resampled MSAs analyzed (Hedges 1992; Pattengale et al. 2010).”