Questions About Fst, Dxy, and Genome-wide π Calculations

[xxxicyixxx]

Hello everyone,

I’ve encountered some issues while using the software. They might seem simple, but I’m unable to resolve them on my own, so I would greatly appreciate your help.

1. Based on average fst across windows #51 and Output Fst variance components #54, I would like to confirm whether the avg_hudson_fst in the results file pixy_fst.txt is calculated using the "average of ratio" method.
2. How are the Fst and dxy values between species pairs computed? Should they be calculated as a direct average of the avg_hudson_fst or avg_dxy values in the results file, or should they be computed using the formula below?
   (window 1 count_diffs + window 2 count_diffs) / (window 1 comparisons + window 2 comparisons)
   3.How should the genome-wide π value for a species be calculated?

Thank you in advance for your guidance!!!