This looks like a great paper. It is the first in a four paper focus on statistical genetics in the latest Nature Review Genetics. It describes and compares 20 or so programs based on what they can be used for, how they can be used, what type of data they can work with, their assumptions, gives links to their online resources, how the same data files can be used with several programs, computation time, etc... can make for great reference material.
Computer programs for population genetics data analysis: a survival guide
Laurent Excoffier and Gerald Heckel
Nature Reviews Genetics 7, 745-758 (October 2006)
Focus on: Statistical Analysis
Abstract: The analysis of genetic diversity within species is vital for understanding evolutionary processes at the population level and at the genomic level. A large quantity of data can now be produced at an unprecedented rate, requiring the use of dedicated computer programs to extract all embedded information. Several statistical packages have been recently developed, which offer a panel of standard and more sophisticated analyses. We describe here the functionalities, special features and assumptions of more than 20 such programs, indicate how they can interoperate, and discuss new directions that could lead to improved software and analyses.