Software: 

ANALYSE, a MacOS application for the analysis of data from structured populations - and especially, clines and hybrid zones. Analyse was written by N. H. Barton and Stuart Baird.

Mathematica packages
  for studying multilocus population genetic models, both numerically and symbolically.   Includes general algorithms for multilocus simulation; multilocus algebra; the coalescent process; estimating genotype frequencies; and a variety of Mathematica utilities.  Written by Nick Barton."

Textbook: 

The Evolution textbook has a website that includes a variety of resources: notes and references, problem sets, ways to explore the literature, links to other sites, and software.