Linkage Programs Installed at Department of Epidemiology

• ACT, i.e., Analysis of Complex Traits
• Mendel 4.11 is installed on penrose2 as of February 2003.
• TDT (Transmission Disequilibrium Tests), can also be found in ACT. Here's its READM file and documentation in MS Word format.
• Sibling-based permutation test
  
• Sibling-based mixed effects model
  
• Allison-and-Beasley-Macro.sas
  
• Joe Terwilliger's original simulation program that once generated GAW data: gaw.p
  Completed with documentation.
• GENEDIVERSITY: Calculates genetic diversity
• Imprint: Software for Analyzing Imprinting and Linkage
• EMLD.tar. A program to calculate pair-wise linkage disequlibrium from genotype data.
  EM algorithm is used to estimate haplotype frequencies.
• SIMLD.tar. A program to simulate linkage disequilibrium between markers within pedigrees as well as association between markers and disease locus. It should be used togeth er with SLINK to achieve the final goal.
• Programs written in R or S+, such as significance.r
• tlinkage is available on cedric. There are four (4) executables: tilink, tmlink, tlinkm, tunk. Sample files are also posted here for testing.
• gassoc is installed onto cedric as of 09/21/2004. You can view documentation here as well as test data
• allegro version 1.2c is installed on cedric as of September 2004. Its documentation is posted here.
• Cluster Tests