Ewens Sampler
Filed in: Perl
A simple perl script to generate the expected site frequency spectrum for a sample of size n for a population mutation rate of θ. I am no longer entirely sure why you would want to do this.
Download ewens.pl
Documentation
A simple perl script to generate the expected site frequency spectrum for a sample of size n for a population mutation rate of θ. I am no longer entirely sure why you would want to do this. Requires Math::BigFloat
To run, type "ewens.pl th n", where n is the sample size, and θ the populaiton mutation rate (4Nμ ). Generates a file "ewens.out".
Example: run "ewens.pl 5 10" and the output file should read:
3.55
1.39
0.66
0.30
0.10
0
0
0
0
0
Which says that one expects a sample of size 10 with a theta of 5 to have 6 alleles. Further, it says that roughly 3-4 alleles are expected to be singletons, 1-2 doubletons, and less than 1 allele is expected to be at higher frequencies.
Note that this script outputs the expectation, not a distribution or confidence interval, and assumes a neutral population in demographic equilibrium following the infinite alleles model of mutation.