Software Download

The Miami Institute for Human Genomics provides research tools to the genetics community to fulfill our mission to discover the genetic and epidemiologic basis of human disease. The Institute is committed to sharing its findings and breakthroughs in technology with colleagues around the world. MIHG-designed software represents one example of how we're partnering with others in a collective effort to understand genetic diseases.

SIMLA Simulation Software
SIMLA 3.2 is a SIMuLAtion program that generates data sets of families for use in linkage and association studies.

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References:
Schmidt M, Hauser ER, Martin ER, Schmidt S. (2005) Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: environmental covariates, gene-gene and gene-environment interaction. Stat Appl Genet Mol Biol. 2005; 4: Article15. Epub 2005 Jun 6.

PDT
The Pedigree Disequilibrium Test (PDT) analysis program allows the user to test for linkage and association in general pedigree data. In addition to allele- and genotype-specific analysis of individual markers. PDT version 5.1 adds the ability to perform genotype-specific analysis over marker.

PDT version 6.0 does not have the ability to perform -specific analysis over marker sets. It is significantly faster than PDT 5.1 and has no restriction on the number of markers or pedigrees.

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References:
Eden R. Martin, S. Monks, L. Warren, N. Kaplan (2000) A Test for Linkage and Association in General Pedigrees:The Pedigree Disequilibrium Test. Am. J. Hum. Genet. 67:146-154, 2000

Letter to the Editor: Correcting for a Potential Bias in the Pedigree Disequilibrium Test. Am. J. Hum. Genet. 68:1065-1067, 2001

APL version 1.1
APL provides a novel test for association in the presence of linkage using general pedigree data.

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For single markers: Martin ER, Bass MP, Hauser ER, Kaplan NL. (2003) Accounting for linkage in family-based tests of association with missing parental genotypes. American Journal of Human Genetics.73:1016-1026.

For haplotypes: Chung R-H, Hauser ER, Martin ER. (2006) The APL test: extension to general nuclear families and haplotypes and the examination of its robustness. Human Heredity. 61:189-199.

For X-chromosome analysis: Chung R-H, Morris RW, Zhang L, Li Y-J, Martin ER (2007) X-APL: An improved family-based test of association for the X chromosome. The American Journal of Human Genetics. 80(1): 59-68.

MDR-Phenomics
MDR-Phenomics aims to detect gene-gene interaction in the pedigree data.

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Reference:
Mei H, Cuccaro ML, Martin ER. Multifactor dimensionality reduction-phenomics: a novel method to capture genetic heterogeneity with use of phenotypic variables. Am J Hum Genet. 2007 Dec; 81(6):1251-61