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.[Link

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.