Linkage disequilibrium assessment software tools | Genome-wide association study data analysis
Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population specific genetic structure as well as functionally mapping regions of disease susceptibility.
A comprehensive suite of tools for haplotype analysis for a wide variety of dataset sizes. Haploview generates marker quality statistics, LD information, haplotype blocks, population haplotype frequencies and single marker association statistics in a user-friendly format. All the features are customizable and all computations performed in real time, even for datasets with hundreds of individuals and hundreds of markers.
Assesses the null hypothesis of linkage equilibrium (LE) for multilocus data. LIAN is based on a Monte Carlo method and an algebraic approach to perform the hypothesis test. It first proceeds by calculating the number of loci at which each pair of haplotypes differs. This web-application then generates pairwise distances between its sampled taxa members and returns the genetic diversity.
Provides a one-stop interface for family-based tests of linkage disequilibrium. QTDT supports a general approach that can accommodate nuclear families of any size, with or without parental information, as well as other tests. The software can use all the information in a pedigree to construct tests of association that are robust in the presence of stratification. It is able to calculate exact p-values by permutation, including when multiple linked polymorphisms are tested.
Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria (LD) between single nucleotide polymorphisms (SNPs). From a data set that provides information on pairwise LD between SNPs in a genomic region, it plots color-coded values of the pairwise LD measurements and returns an object containing several components. The package also contains two functions which can be used to highlight or mark with a symbol pairwise LD measures on an LD heat map.
Deduces population admixture by the calculation of weighted linkage disequilibrium (LD) statistics. ALDER is an application based on a fast Fourier transform (FFT) algorithm with the aim of: (i) increasing the speed of admixture LD analysis, (ii) improving robustness of admixture date inference, and (iii) exploiting results as a resource about history. The software also includes a feature to determine the affine term that uses inter-chromosome single nucleotide polymorphism (SNP) pairs.
Allows users to query pairwise linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs). LDlink is a web-based LD analysis tool providing access to several bioinformatics modules. The software integrates expanded population reference sets, updated functional annotations, and interactive output to explore possible functional variants in high LD. It can facilitate mapping of disease susceptibility regions and assist researchers in characterizing functional variants based on genotype-phenotype associations with potential clinical utility.
Finds proxy single nucleotides polymorphisms (SNPs) based on linkage disequilibrium (LD). SNAP includes features to: (i) detect SNP proxies in genes, (ii) shape fine mapping boundaries, (iii) verify SNPid aliases along dbSNP builds, (iv) determine annotations for SNPs of interest or (v) create association and graphical plots of proxies for a queried SNP. It aims to assist users in performing cross- genome-wide association studies (GWAS) comparisons.