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Software

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

APL

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

CAPL

CAPL, the Combined Association in the Presence of Linkage test is a powerful association method that can accommodate family and case-control data and account for population stratification. It allows for missing parental genotypes and multiple affected siblings in nuclear families. This download includes the source code, documentation, examples and Windows binaries.

APL-OSA version 1

In the presence of genetic heterogeneity, APL-OSA can identify a genetically homozygous subset of families based on a trait-related covariate.

Combined Likelihood Ratio Test for Candidate Gene Studies

The LRT The Combined Likelihood Ratio Test is an extension of the original likelihood ratio test (LRT) proposed by Weinberg, et. al. (1999) to test child genotype risk, maternal genotype effects and parent-of-origin effects. (Windows only.)

EMK

The EMK program implements two family-based association methods, allele- and genotype- based association methods, that we developed based on the framework of the allele-based method developed by Monks and Kaplan (2000) for quantitative traits (Li et al. 2008)

Genetic Association Tests based on Ranks (GATOR)

GATOR implements the family-based association method for quantitative traits with and without censoring described in Allen et al. (2006). It can handle quantitative phenotypes with skewed distributions, censored data, and/or outliers. Currently the program focuses on bi-allelic markers (e.g. single nucleotide polymorphisms). GATOR is able to perform association tests using four different genetic models: general, dominant, recessive, and additive.

Ordered Subset Analysis Program

The OSA program is the product of collaboration between the University of Michigan and the Duke Center for Human Genetics. OSA tests for linkage in heterogeneous data sets by taking covariate data into account. Co-variates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, etc. (Solaris and Linux only.)

Ordered Subset Analysis for Case-Control Data Program

The OSACC program was designed to evaluate evidence for association in the presence of genetic heterogeneity.

PDT Analysis Program

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 sets.

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.

SIBLINK v 3.0

The SIBLINK program performs linkage analysis on affected sib-pairs.

SIMLA Simulation Software

SIMLA is a SIMulation program that generates data sets of families for use in linkage and association studies.

SIMLA_3.3 with GUI

SIMLA_3.3 with GUI adds a graphical frontend to SIMLA3.2 (included) to assist users in creating a control file.

SIMLAPLOT

SIMLAPLOT is a tool designed to help visualize the joint effect of genes and continuous environmental covariates on simulation models.

X-LRT

The X-LRT a suite of family-based tests for detecting association of X-chromosome genes.

XQTL

XQTL is a family-based allelic/haplotype association test for quantitative traits using X-linked SNP/two-locus markers in a nuclear family design.

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