Core Programs

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.

• SIMLA Simulation Software
  
• SIMLA_3.2
  
• SIMLA WITH GUI
  
• SIBLINK v 3.0
  
• PDT Analysis Program v 5.1
  
• APL-OSA Beta Version
  
• APL version 1.1
  
• Ordered Subset Analysis Program
  
• Combined Likelihood Ratio Test for Candidate Gene Studies
  
• GATOR
  

SIMLA Simulation Software

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

SIMLA_3.2

SIMLA_3.2 is a major upgrade to versions 2.3 and 3.0 that provides the ability to simulate two disease loci and two environmental covariates. Gene-gene and gene-environment interactions may also be simulated which jointly determine the disease risk of all pedigree members.

SIMLA_3.3 with GUID

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

SIBLINK v 3.0

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

PDT Analysis Program v 5.1

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 (Solaris, Linux, Windows).

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.

APL version 1.1

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

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.)

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.)

Genetic Association Tests based on Ranks (GATOR)

GATOR is a program that implements the family-based association method for quantitative traits with and without censoring described in Allen et al. (2006). This program is distinctive in that 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). It can handle parent-offspring (Triads), sibships with (Quads) and without (Sibs) parents, and extended multi-generation pedigree data (General Pedigree). GATOR is able to perform association tests using four different genetic models: general, dominant, recessive, and additive.

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