We have developed a number of analytical tools for use in simulating DNA sequence data under a number of coalescent models, examining the power of various statistical approaches for dissecting complex traits, and analyzing high density array data. The tools are largely written in C, but we have put web based front ends on these tools using PERL and CGI. We have also developed an open-source, high-throughput SNP (single nucleotide polymorphism) genotyping system. Below are links to these tools.

HIGH-THROUGHPUT SNP GENOTYPING
Association mapping studies aim to identify polymorphic sites contributing to phenotypic variation. To achieve high power, and enable the detection of subtle-effect genetic factors, very large numbers of genotypes must be collected. We have developed a cost-effective solution to this problem, and provide step-by-step instructions on the implementation of this technology.

COALESCENT PROCESS TOOLS
These tools are based on coalescent theory and can be used to simulate samples of gametes from populations under different genetical and demographic models. Extensions to the coalescent allow estimates of the power of different types of association studies.

QTL MAPPING TOOLS
Our QTL mapping tools allow the user to apply popular mapping methods to simulated populations and to thereby evaluate those methods.

STATISTICAL TESTS
In many instances it is important to assess the statistical support for an association between molecular markers and variation in a complex trait. This link allows the user to apply a number of the tests we have found to be of use.

HIGH DENSITY ARRAYS
High density arrays are a very powerful new tool for molecular biologists. Here are links to tools used in the analysis of high density array data.