prfreq

[…] utilized for processing genotypes and allele frequency spectra.To test for the influence of selection on the allele frequency spectrum of CNVs, we used a Poisson Random Field approach implemented in prfreq , which evaluates the expected allele frequency distributions given different demographic and selection models. We compared the estimates of the scaled selection coefficient γ of CNVs (both del […]

[…] oth the French and French-Canadian populations. First, we estimated the demographic parameters and the population selection parameter (γ = Ne(s)) using the Poisson Random Fields method implemented in prfreq . To estimate population demographic parameters, we used synonymous sites to test different demographic models and we find a significantly better fit for models that include a bottleneck and ex […]

[…] ectrum (SFS) from the global sample of M.tb is shown in the SFS is leptokurtic, with an irregular decay in the frequency of minor alleles as the counts increase. Results of analyses of the SFS using prfreq are shown in . The likelihood of the observed synonymous SFS was estimated for constant size, instantaneous expansion and exponential models of growth. The best fit growth model is of a sudden […]