We were looking for genetic diversity in the exon level of an MHC transcript. We used ANGSD to calculate Thetas, Tajima and Neutrality tests and one of the thetas was a pairwise theta, however I am unsure what this means and how it differs from Tajima's D? http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests
We then divided the tP over length of each exon to find genetic diversity in the exon level. However, as I am very interested in statistics, if someone could explain what the tP statistic means exactly it would be highly appreciated.