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As in the case of the LS-based bootstrapping, the normalized secondary bootstrap scores can be computed and used to estimate the tree robustness.
The standard non-parametric bootstrap scores can be calculated using the following procedure [ 2]: (1) l columns of A are randomly chosen with replacements, giving rise to a pseudo-replicated sequence alignment PRA with n rows of l columns.
Steps 3 and 4 were then carried out as described above using the normalized LS coefficients, and the weight of the tree t was computed as follows: (8) Secondary bootstrap scores can be also used to assign weights to phylogenies inferred from pseudo-replicates.
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After that the scores can be counted.
Normalized LS-based bootstrap scores can also be computed and used to estimate the robustness of a phylogenetic tree.
Goal scoring can be a streaky business.
Alternatively, a bootstrap approach can be followed.
In the latter case, bootstrap support can be misleading.
Bootstrap solutions can be found in 11 and 12.
In principle, the bootstrap strategy can be expanded accordingly.
We developed a nonparametric bootstrap similar to standard bootstraps used for phylogenetic reconstructions, and also a parametric bootstrap that can be scaled to very large genomes.
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Justyna Jupowicz-Kozak
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