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Sliding window analysis including non-coding regions also showed comparable values (Supplementary Table 4).
Moreover, time window analysis showed significant changes in the figure of merit at different time binning (Supplementary Fig. 5).
Using the heterozygous sites called within a diploid organism, we performed a sliding window analysis of the genetic diversity θ (4 Nμ) along the genome for each individual.
A moving window analysis is used in this method.
To confirm our results from sliding window analysis we used a software package called SWAPSC, which similarly uses a sliding window analysis procedure to calculate selective constraint [54].
A sliding window analysis over EGFR revealed three signals within intron 1 (Supplementary Figure S2).
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The effect is inherent in the method and affects many applications of sliding-window analysis.
We also discusses similar problems when sliding-window analysis is used in several other applications in molecular evolutionary studies.
The trial-and-error approach was an attempt to guide against the high false positives of the sliding-window analysis.
Results from the spline-window analysis were compared to those of the previously published sliding-window analysis to determine the degree of overlap between the methods.
Therefore, inflection points are treated as window boundaries and a distinct-window analysis proceeds.
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