BackgroundNon-parametric bootstrapping is a widely-used statistical procedure for assessing confidence of model parameters based on the empirical distribution of the observed data [] and, as such, it has become a common method for assessing tree confidence in phylogenetics []. Traditional non-parametric bootstrapping does not weigh each tree inferred from resampled (i.e., pseudo-replicated) sequences. Hence, the quality of these trees is not taken into account when computing bootstrap scores associated with the clades of the original phylogeny. As a consequence, traditionally, the trees with different bootstrap support or those providing a different fit to the corresponding pseudo-replicated sequences (the fit quality can be expressed through the LS, ML or parsimony score) contribute in the same way to the computation of the bootstrap support of the original phylogeny.
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