The software offered below was written by Paul O. Lewis unless otherwise indicated. Most are useful for teaching concepts in statistics or phylogenetics, and all are free for downloading. Unfortunately (as one person doing this in my spare time) I can offer very little in the way of support for these programs. You are welcome to email me; however, I cannot guarantee that I will have time to address your query (or even answer your email!). I do make an honest effort to respond to reasonable requests for help.

Note that these programs are offered AS IS with absolutely NO WARRANTY of any kind.

 
Hickory Program by Kent E. Holsinger and Paul O. Lewis that provides for Bayesian estimation of F-statistics from both dominant and co-dominant marker data.
GDA Program by Paul O. Lewis and Dmitri Zaykin designed to accompany the book "Genetic Data Analysis" by Bruce S. Weir (1996, Sinaur Associates). Computes linkage and hardy-weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics. On 11 January 2008 I changed the download format from self-extracting zip archive to a simple zip archive. Let me know if this causes problems. The new zip file contains an additional example data file (fbi99.nex) included at the request of Bruce Weir to accompany his forthcoming review paper.

Chris Basten has compiled a command-line-only version of GDA that runs under Mac OS 10.2.8 and 10.3 (Jaguar and Panther). This version can be downloaded here. After downloading, you should open a terminal window, navigate to the folder containing the file, and type "chmod +x gda1.1" to make GDA executable.
 
Source Code Libraries
 
NCL A C++ class library for reading data files formatted in the NEXUS file format common to several phylogenetic analysis software applications.
 
 
CLT Illustrates the fact that sums of just about anything are approximately normally distributed (for those of us who really want to believe the Central Limit Theorem, but who need to see it to believe it).
LBA Animates the long branch attraction example in Joe Felsenstein's classic 1978 paper entitled "Cases in which parsimony or compatibility methods will be positively misleading".
Brownian Illustrates the Brownian motion model used by Joe Felsenstein in his classic 1985 paper "Phylogenies and the comparative method" (the paper that introduced his Phylogenetically Independent Contrasts).
Diffusion Illustrates simple diffusion
Osmosis Illustrates concept of a semipermeable membrane (smaller particals diffuse across barrier but larger ones cannot)
Crossover Simulates crossing over between homologous chromatids and is designed to aid in understanding the notion of the recombination fraction and its use in constructing linkage maps.
Bulbs Illustrates a simple failure model using a simulated bank of light bulbs.
 
Microsoft® Windows® Applications for Teaching
 
Adares Teaching application useful for illustrating the adaptive rejection sampling approach used for gibbs sampling in Bayesian statistics.
ChisCalc Chi-square significance probability calculator
Bayesian Coin Tosser Illustrates Bayesian concepts of prior and posterior densities for a simple coin flipping example.
FSim Graphically illustrates the concept of inbreeding coefficient.
MCRobot Illustrates the basic principles of Markov chain Monte Carlo simulation, using arbitrary, user-defined landscapes composed of one or more bivariate normal densities.
MLCalc A calculator useful in demonstrating the estimation of evolutionary distances using the method of maximum likelihood under four simple substitution models.
ThetaSim Graphically illustrates the concept of population differentiation due to isolation and genetic drift.