Post date: Jul 06, 2020 7:35:57 PM
the distribution of the variant frequencies of a given set of loci in a population.
Histogram with the total number of loci with a given frequency:
- for each locus, if ancestral version of the allele --> 0, if variant --> 1
- calculate the number of 1 per locus --> variant frequency
- pool together the variants with the same frequency in a histogram.
Indices such as Tajima's D, Watterson and Fst.
We can estimate the expected allele frenquency spectrum: we know the rate of mutation per site, and the time since divergence. Deviation from neutrality or demographic equilibirum will change the shape of the spectrum.