Software


HS-TDT
You can download HS-TDT for Windows here, and HS-TDT for Unix here.

  • The program HS-TDT implements the haplotype sharing TDT methods proposed by Zhang et al. (2003; Am J Hum Genet 73:566-579), Zhang et al.(2004;Am J Hum Genet 74: 591-593), and Sha et al. (2004) ( pdf file) to test for association using tightly linked markers for general nuclear family data. It allows missing genotypes and aplicable both to quantitative traits and qualitative trait. By merging the rare haplotypes, it can well control the false-positive results caused by genotyping errors (Sha et al. 2004).

  • It also can estimate the haplotype frequencies based on nuclear family data. The method implemented in this version of HS-TDT uses Partition-Ligation EM algorithm to estimate haplotype frequencies by incorporating nuclear family information. The program allows missing genotype, missing parents, and can deal very large number of markers.


ELA
You can download ELA for Windows here, and ELA for Linux here.

  • The program ELA implements a genetic association mapping method for complex diseases [Zhaogong Zhang, Shuanglin Zhang, Man-Yu Wong, Nicholas J. Wareham, Qiuying Sha (2007) An Ensemble Learning Approach Jointly Modeling Main and Interaction Effects in Genetic Association Studies. Genetic Epi. Submitted]. The method implemented in this version of ELA uses an Ensemble Learning Approach (ELA) to jointly model main and interaction effects in genetic association mapping. The program allows missing genotypes and can deal with very large number of markers. The detail methods used are introduced in the above mentioned paper.

IPEM
You can download IPEM for Windows here and IPEM for Linux here.

  • In genome-wide association sudies, some causal variants may be completely untyped in that only the tagging single nucleotide polymorphisms (SNPs) are genotyped. This algorithm imputes the genotypes at untyped marker loci in a new study. It utilizes an available comprehensice reference haplotype dataset and incorporates the inherent multi-locus linkage disequilibrium. This software can impute the genotypes on 500,000 SNPs in 500 individuals within 32 hours.