MC-PDT (Monte Carlo Pedigree Disequilibrium Test) is a R package that performs linkage disequilibrium test and parent-of-origin tests in the presence of association using pedigree data. Families with missing genotype data are allowed; Monte Carlo samples of the missing genotypes conditional on the observed data will be used.
ALDER (Admixture-induced Linkage Disequilibrium for Evolutionary Relationships) is a software package that computes weighted linkage disequilibrium (LD) curves, which can be used to infer admixture parameters including dates, mixture proportions, and phylogeny.
GOLD ( Graphical Overview of Linkage Disequilibrium) provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data.
QTDT (Quantitative and Discrete Traits) provides a convenient one-stop interface for family based tests of linkage disequilibrium. The general models can be used to analyse quantitative or discrete traits in nuclear families, with or without parental genotypes, or extended pedigrees. In addition, QTDT can calculate exact p-values by permutation even when multiple linked polymorphisms are tested.
LDSO (Linkage Disequilibrium with Several Options) is a completely self-contained program written in Fortran90. It is a complete computer program for simulations of whole diploid population histories under various historical scenarios based on the gene-dropping method (MacCluer et al. 1986). The random number generator from L’Ecuyer (1996) was used. The genetic history of one or two populations can be simulated; the output files can deliver various statistics (inbreeding rates, allele frequencies, linkage disequilibrium) on these populations for generations wished by the user. Evolutionary forces that are classically found in livestock populations, such as mutation, selection, changes in the population size or random drift, can be taken into account.
LD Select analyzed the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2.
At each round of selection, the binning algorithm identifies the single SNP which exceeds the threshold r2 with the maximum number of other SNPs, and sets this group of SNPs as a bin. Then each SNP within the bin is analyzed to determine whether it exceeds the threshold r2 with all other SNPs in the bin. All SNPs in a bin that meet this criterion are designated as TagSNPs. Only one TagSNP needs to be typed per bin.
DMLE (Disease Mapping using Linkage disEquilibrium) is a software of high-resolution mapping of the position of a disease mutation relative to a set of genetic markers using population linkage disequilibrium (LD).