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Genetic distances were measured as pairwise allele differences among Moroccan haplotypes and 10,000 bootstrap permutations were applied to determine the significance of groups using MEGA v5.05 [ 48].
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In running GSEA for each gene set, 1,000 permutations were applied.
One thousand permutations were applied in an unpaired filtered data set.
The circular genomic permutation was applied to a small study (N = 719 individuals).
To explore how circular permutations perform compared with random permutations, alternative permutation strategies were applied to the distance 0 dataset.
To evaluate branch robustness of trees, parsimony-based bootstrap analyses were applied.
For NJ and ME 1000 bootstraps and for ML 100 bootstraps were applied.
Permutation tests were applied for adjusting statistics for multiple comparisons: a total number of 1,000 permutations were performed for each test.
Permutation tests were applied to check for overtraining.
500 non-parametric bootstraps were applied for robustness measures.
Resampling and permutation methods were applied to investigate temporal clustering of outbreaks.
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