Dear all,
Finally... I started a refreshment of the bpp-popgen library. Classes are now structured in subdirs as the other libraries. I also tweaked a few things here and there. On that occasion, I added a new example program in bppSuite, called bppPopStats, which can compute a variety of population statistics on an alignment (a kind of DNASP, but command line), including various theta estimators, Tajima's D, Fu & Li's D and F, and more are to come (MK test, etc). As a result, bppsuite now requires bpp-popgen to compile.
Cheers,
Julien.