All of the software used in this course is available without charge. I've used the Windows and Linux versions for all of them, and the Mac versions for some of them. If you run into problems, I'll help as much as I can.

Arlequin
Version 3.5.1.2 is available as a self-installing executable for Windows and as a command-line version for Linux. There's a version for Mac OS X (v10.5 or greater) available here

GDA

No registration. GUI executable available for windows. Command-line version for Mac OS X from the GDA page. Snow Leopard GUI available here (for those within the UConn.edu domain).

Hickory

Registration is requested. Executables and source code (C++) are available for Windows and Linux (x86).

IM

No registration. Executable available for Windows.

Structure

Registration is requested. Executables are available for Windows, Linux (x86), and Mac OS X.

QTL Cartographer

Registration is not necessary. Executables are available for Windows, Linux (x86), and Macintosh. Only the Windows version provides a user friendly graphical user interface.

R

Registration is not necessary. Source code (C and Fortran) and executables are available for a variety of platforms. R is a general purpose package for statistical analysis. It is very powerful and very flexible, but if you're used to SAS, SPSS, or something similar, it will take a little getting used to.

WinBUGS

Registration is required. Executables are available for Windows. There's a version of OpenBUGS for Mac OS X (v10.5 or greater) here.

JAGS (Macintosh)

JAGS is a command-line program that implements the same models analyzed in WinBUGS. If you have a Mac, a very good alternative to running WinBUGS through Wine is to run JAGS through R. Download JAGS-1.0.4u.dmg from the directory at this link, and install in the usual way. JAGS is also available for Windoze and Linux. Ask me about it if you're interested.

Other resources

Additional software resources

Links to a variety of additional software that may be useful in analysis of some types of population genetic data.

Java simulations used in the course

Links to the various simulations used in lecture, e.g., estimating frequencies at the ABO locus using the EM algorithm, the Wahlund effect, genetic drift, and natural selection.

Summer Institute in Statistical Genetics

A series of 2 1/2 day workshops on a variety of topics in statistical genetics. Held on the campus of the University of Washington. Some tuition and travel scholarships are available for students (undergraduate, graduate, and postdoctoral).

Bayesian Population Genetic Data Analysis

Notes, data sets, and WinBUGS code from Bayesian parts of the Population Genetics Data Analysis module of the Summer Institute in Statistical Genetics.

Selected books on population genetics

Bulmer, M. G. 1985. The Mathematical Theory of Quantitative Genetics. Clarendon Press, Oxford.

Cavalli-Sforza, L. L., and W. F. Bodmer. 1971. The Genetics of Human Populations. W. H. Freeman and Co., San Francisco, CA.

Christiansen, F. B., and M. W. Feldman. 1986. Population Genetics. Blackwell Scientific Publications, Palo Alto, CA.

Crow, J. F. 1986. Basic Concepts in Population, Quantitative, and Evolutionary Genetics. W. H. Freeman and Co., San Francisco, CA.

Crow, J. F., and M. Kimura. 1970. An Introduction to Population Genetics Theory. Harper & Row, New York, NY.

Doolittle, D. P. 1987. Population Genetics: Basic Principles. Springer-Verlag, Berlin.

Durrett, R. 2002. Probability Models for DNA sequence evolution. Springer-Verlag, Berlin.

Edwards, A. W. F. 2000. Foundations of Mathematical Genetics. Cambridge University Press, Cambridge, UK.

Ewens, W. J. 2004. Mathematical Population Genetics. I. Theoretical Introduction, 2nd ed. Springer-Verlag, Berlin.

Falconer, D. S., and T. F. C. Mackay. 1996. Introduction to Quantitative Genetics, 4th ed. Longman, London.

Fisher, R. A. 1958. The Genetical Theory of Natural Selection, 2nd revised ed. Dover Publications, Inc., New York, NY.

Gale, J. S. 1990. Theoretical Population Genetics. Unwin Hyman, London.

Gillespie, J. H. 1991. The Causes of Molecular Evolution. Oxford University Press, New York, NY.

Gillespie, J. H. 1998. Population Genetics: A Concise Guide. Johns Hopkins University Press, Baltimore, MD.

Haldane, J. B. S. 1932. The Causes of Evolution. Longmans, Green, & Co., Ltd., London.

Halliburton, R. 2004. Introduction to Population Genetics. Pearson Prentice Hall, Upper Saddle River, NJ.

Hartl, D. L., and A. G. Clark. 1997. Principles of Population Genetics, 3rd ed. Sinauer Associates, Sunderland, MA.

Hedrick, P. W. 2000. Genetics of Populations, 2nd ed. Jones and Bartlett Publishers, Sudbury, MA.

Hein, J., M. H. Schierup, and C. Wiuf. 2005. Gene Genealogies, Variation, and Evolution. Oxford University Press, New York, NY.

Kearsey, M. J., and H. S. Pooni. 1996. The Genetical Analysis of Quantitative Traits. Chapman & Hall, London.

Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.

Lange, K. 2002. Mathematical and Statistical Methods for Genetic Analysis. Springer, New York.

Lewontin, R. C. 1974. The Genetic Basis of Evolutionary Change. Columbia University Press, New York, NY.

Li, C. C. 1955. Population Genetics. University of Chicago Press, Chicago, IL.

Li, W.-H., and D. Graur. 1991. Fundamentals of Molecular Evolution. Sinauer Associates, Sunderland, MA.

Li, W.-H. 1997. Molecular Evolution. Sinauer Associates, Sunderland, MA.

Lynch, M., and B. Walsh. 1998. Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.

Mather, K., and J. L. Jinks. 1982. Biometrical Genetics, 3rd ed. Chapman and Hall, London.

Maynard Smith, J. 1989. Evolutionary Genetics. Oxford University Press, New York, NY.

Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, NY.

Nielsen, R., ed. 2005. Statistical Methods in Molecular Evolution. Springer-Verlag, Berlin.

Rice, S. H. 2004. Evolutionary Theory: Mathematical and Conceptual Foundations. Sinauer Associates, Sunderland, MA.

Roff, D. A. 1997. Evolutionary Quantitative Genetics. Chapman & Hall, New York, NY.

Sorensen, D., and D. Gianola. 2002. Likelihood, Bayesian, and MCMC Methods in Quantitative Genetics. Springer-Verlag, Berlin.

Spiess, E. B. 1989. Genes in Populations, 2nd edition. John Wiley & Sons, New York, NY.

Templeton, A. R. 2006.  Population Genetics and Microevolutionary Theory. John Wiley & Sons, New York, NY.

Wakeley, J.  2009.  Coalescent Theory: An Introduction. Roberts & Company Publishers, Greenwood Village, CO.

Weir, B. S. 1996. Genetic Data Analysis II. Sinauer Associates, Sunderland, MA.

Wright, S. 1968-1978. Evolution and the Genetics of Populations, 4 vols. University of Chicago Press, Chicago, IL.