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All remaining alignments were screened for the presence of phylogenetic signal using the Permutation Tail Probability (PTP) test [ 32, 33].
Using the permutation tail probability tests we found that the topology of the tree reflected both the pattern of resistance to metronidazole (the major anti-trichomonal drug) (p < 0.01) and the pattern of infection of strains by mycoplasmas (p < 0.05).
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For the group analysis, we used the permutation tool "randomise" with 5000 permutations (Nichols & Holmes, 2002).
Using the permutation test method, with 10,000 permutations, we found 10 miRNAs were strongly correlated with survival (p≤0.005).
Correction for multiple testing was conducted using the permutation method.
Lower row: new MVPA results using the permutation framework.
These measures include the permutation tail probability test (PTP [22] [24]), the phylogenetic bootstrap [25], the consistency and retention indices [26] [29], and the network-derived delta index [30], [31].
All alignments passed the permutation tail probability (PTP) test [ 34] (Table 1).
We used the permutation test (1000 permutations) to estimate P-values.
Empirical P-values were derived using 1000 permutations using the incorporated permutation feature of WebQTL.
The q-value was calculated using the SAM permutation scheme with 1,000 permutations.
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