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For kernel density estimation, the empirical probability distribution implementing the Variable Kernel Method with Gaussian Smoothing of the Apache Commons Math 3.6 API [15] is used.
To investigate this possibility, we reanalyzed the data by replacing the parametric distribution implementing the null hypothesis in the original UE analysis by a distribution derived from surrogates.
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The current distribution, implemented entirely in JAVA, includes a binary release of the AMOS system developed at Columbia for MPEG-4 semantic video object segmentation.
To test for genomic enrichment we used a method that tests for the local enrichment of lead variants and those in LD with genomic features by randomly shifting annotations to generate a null distribution; implemented in GoShifter32.
However, as GCP setting over high relief area or the unbalanced GCP distribution implemented by semi/full-automated GCP selection might result in instability of sensor model occasionally, the GCP selection was performed manually in this paper in order to achieve an accurate geodetic control.
Reduction in rare allele numbers was tested using a qualitative descriptor of allele frequency distribution implemented in BOTTLENECK [71].
The amino acid substitution rate was shaped by the Γ distribution implemented by the program.
Statistical significance was assessed using the chi-squared test and the functional enrichment statistics was calculated using the hypergeometric distribution implemented in the R package.
Testing the probability of shared polymorphisms arising via gene conversion vs. independent mutation utilized the approximation of the hypergeometric distribution (implemented in DNASP; method described in [ 26]).
Genes significantly overrepresented in the target lists were identified using the statistics (hypergeometric distribution) implemented in the 'GO browser' of Spotfire DecisionSite for Functional Genomics.
Divergence times were estimated using a relaxed-clock method with substitution rates sampled from an uncorrelated lognormal distribution implemented in BEAST v. 2.1.3 [ 37].
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