Here is a simple annotated script to quickly calculate, output, and graph allele frequencies in R. Here I have downloaded data (via dryad) from Lander et al. 2011 of a European Beech data set genotyped at 13 microsatellite markers. I have used a single population as the example data set.
Here is the output from the script at one locus:
and here is a plot of allele frequencies at a different locus: Allele frequency plot
Please keep in mind that this is only one example of how to calculate allele frequencies. Feel free to add your own suggestions or improvements in the comments. If anybody has a script that calculates unbiased allele frequencies (with respect to sample size), I would be happy to post that as well.