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On the H1 phylogeny, the 5 H1N2 viruses collected from swine in Brazil during 2011 also are monophyletic, although the clade is supported by just below the 70% bootstrap threshold on the ML tree (64% bootstrap support, Technical Appendix Figure 2) and 80% posterior probability threshold on the MCC tree (79%, Figure 3).
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However, the bootstrap threshold algorithm differs from the empirical permutation threshold algorithm as the former generates a new data set based on a bootstrap re-sampling of the centered residual effects.
All trees were set at a bootstrap threshold of 50% and rooted using T. gratilla as the outgroup.
Bootstrap values on the consensus trees were derived from 1000 bootstrap replicates.
Moreover, if we switch to the bootstrap, precision depends on the number of bootstrap samples.
The most popular approach to obtaining polytomies is through forcing a threshold on bootstrap values of branches generated from a consensus tree, which is produced from a set of gene trees based on different selections of gene subsets.
We calculated the proportion of estimates lying outside the ±0.01 absolute change threshold on resampling using 2000 non-parametric bootstrap samples.
Bootstrapped confidence intervals on the parameter estimates were calculated based on 5,000 randomly bootstrapped samples.
Bootstraps on the mean, median, variance, skewness and kurtosis of these distributions are performed.
If the threshold can not be found theoretically, we can do parametric bootstrap to find the threshold.
The bootstrap approach is based on the assumption that the bootstrap distribution is similar to the sample distribution.
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