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We attempted to take the demographic history of these species into account by using simulated replicates of estimates of D. melanogaster African population dynamics (Hutter et al. 2007; Duchen et al. 2013) to determine our significant SweeD cutoff points.
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Using simulated variation of experimental designs, we found that biological replicates are critical for statistical analysis of Bar-seq data, whereas technical replicates are of less value.
Significance was assessed using 1000 simulated replicates and departures from neutrality were interpreted as consistent with population growth.
Posterior predictive p-values allow us to average over the uncertainty in θ and γ using M simulated replicated datasets (x∗) from the predictive distribution of the data.
One SNP per gene, with the lowest P-value, was included in the ALIGATOR analysis using 20 000 simulated replicate gene lists and 5000 simulated replicate studies.
All ALIGATOR analyses used 10 000 simulated replicate gene lists and 2000 simulated replicate studies.
The DOE used simulated and sampled data.
We apply likeLTD to lab-based profiling replicates, simulated replicates, and replicates obtained by re-sampling the five actual replicates of a real CSP.
We compare the observed mean frequency with 10,000 simulated replicates.
The association analysis was repeated for each simulated replicate.
Bootstrapping was assessed by using 1,000 replicates.
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