For details on the H statistic see
Fay and Wu 2000.
Any questions or difficulties contact me at jfay(a)genetics.wustl.edu
Enter the sample size:
[2:5000]
Enter the recombination rate: [0:100]
Here, the size of the region and 4Nc is for 1kb. So to get 4Nc/bp = 0.001 enter 1 above. 
Enter the number of simulations: [1:100000]
Enter the probability of backmutation: [0:0.5]
Generally, the rate of divergence at synonymous sites divided by 3 is the probability of a backmutation (see paper for details). Divergence between D. melanogaster and D. simulans is typically between 0.05  0.10, and divergence between humans and chimpanzees is typically between 0.007  0.012.

Enter the frequencies of segregating sites of various types:
Example: f1=3 f2=2 f3=1 f8=1 f9=1; where, for example, f1=2 means that the number of mutations of size 1 (externalmutations) is 2.

The results of the Hstatistic are now scaled by the variance of the statistic. For more information see Zeng, Shi, Fu and Wu PDF
To run one of Fu's test see Fu's Website
For more population genetic analysis software see molpopgen.org
Source code htest.tgz
