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The software included are listed bellowIMPUTE 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] v1.0.0v2.1.0 19-07-200920-01-2010 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 databetween the PED file format and the FILE FORMAT used by SNPTEST and IMPUTE. v0.6.0 07-07-2009