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TASSEL – software to evaluate linkage disequilibrium, traits associations, and evolutionary patterns rAggr – finds proxy markers (SNPs and indels) that are in linkage disequilibrium with a set of queried markers, using the 1000 Genomes Project and HapMap genotype databases.
Arlequin is a free population genetics software distributed as an integrated GUI data analysis software. [1] It performs several types of tests and calculations, including Fixation index (F st, also known as the "F-statistics" [2]), computing genetic distance, Hardy–Weinberg equilibrium, linkage disequilibrium, analysis of molecular variance, mismatch distribution, and pairwise difference tests.
In genetics, association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes (observable characteristics) to genotypes (the genetic constitution of organisms), uncovering genetic associations.
Haploview [1] is a commonly used bioinformatics software which is designed to analyze and visualize patterns of linkage disequilibrium (LD) in genetic data. Haploview can also perform association studies, choosing tagSNPs [2] and estimating haplotype frequencies.
The software is designed flexibly to perform a wide range of basic, large-scale genetic analyses. PLINK currently supports following functionalities: data management; basic statistics (F ST, missing data, tests of Hardy–Weinberg equilibrium, inbreeding coefficient, etc.); Linkage disequilibrium (LD) calculation;
Snagger is a bioinformatics software program for selecting tag SNPs using pairwise r 2 linkage disequilibrium. [1] It is implemented as extension to the popular software, Haploview, and is freely available under the MIT License. [2]
In statistical genetics, linkage disequilibrium score regression (LDSR [1] or LDSC [2]) is a technique that aims to quantify the separate contributions of polygenic effects and various confounding factors, such as population stratification, based on summary statistics from genome-wide association studies (GWASs).
Linkage disequilibrium (LD) and association mapping is receiving considerable attention in the plant genetics community for its potential to use existing genetic resources collections to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest (Yu and Buckler, 2006). The three elements of particular ...