ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Thetas,Tajima,Neutrality tests
Angsd can estimate the Tajimas D and other neutrality test. Method works by using the posterior allele frequencies for every site, and uses these for calculating different per-site estimates of theta. Due to the linearity the population scaled mutation rate is therefore the sum of the per-site estimates