The software included are listed bellow
| IMPUTE | a program for genotype imputation in genome-wide association studies and fine-mapping studies based on a dense set of marker data (such as HapMap) [2,5] | v1.0.0 v2.1.0 | 19-07-2009 20-01-2010 |
| SNPTEST | a program for Frequentist and Bayesian tests of SNP association with binary (case-control) and quantitative phenotypes that takes genotype uncertainty into account [2] | v2.1.0 | 20-03-2010 |
| HAPGEN | a program to simulate case control datasets at linked SNP markers conditional upon a set of known haplotypes [4] | v1.3.0 | 17-01-2008 |
| META | a program to carryout meta-analysis of genetic studies. | v1.0.0 | 12-10-2009 |
| GENECLUSTER | a program for location and detection of unobserved causal loci in fine-mapping experiments and genome-wide association studies. | v1.0.0 | 19-03-2010 |
| CHIAMO | a genotype calling algorithm for multi-cohort studies [1] | v0.2.1 | 22-10-2007 |
| GTOOL | a program for (a) generating subsets of genotype data, and (b) converting genotype data between the PED file format and the FILE FORMAT used by SNPTEST and IMPUTE. | v0.6.0 | 07-07-2009 |