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Linkage disequilibrium assessment software tools | Genome-wide association 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. Source text: Machiela and Chanock,…
LDstore
Desktop

LDstore

Enables sharing of linkage disequilibrium (LD) information needed for accurate…

Enables sharing of linkage disequilibrium (LD) information needed for accurate fine-mapping in the era of biobank-scale datasets. LDstore serves for estimation, storage, and seamless sharing of LD…

LDetect
Desktop

LDetect

A method to identify approximately independent blocks of linkage disequilibrium…

A method to identify approximately independent blocks of linkage disequilibrium (LD) in the human genome. These blocks enable automated analysis of multiple genome-wide association studies.

LOCO-LD
Desktop

LOCO-LD LOcalization COrrection using LD

Uses a probabilistic model to describe the allele frequencies and the linkage…

Uses a probabilistic model to describe the allele frequencies and the linkage patterns within short genomic windows. LOCO-LD is an approach to performing spatial localization corrected for…

AVENGEME
Desktop
LDlink
Web
Desktop

LDlink

Allows users to query pairwise linkage disequilibrium (LD) between single…

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.…

STOPGAP
Desktop

STOPGAP Systematic Target OPportunity assessment by Genetic Association Predictions

Contains genetic associations and genes that influence human traits. STOPGAP is…

Contains genetic associations and genes that influence human traits. STOPGAP is a genetic association and functional genomics data to supply more evaluation of the gene scores and variant-to-gene…

QMSim
Desktop

QMSim

Simulates large-scale genotyping data in multiple and complex livestock…

Simulates large-scale genotyping data in multiple and complex livestock pedigrees. QMSim helps to validate new approaches for fine mapping and genomic selection. The simulation is basically carried…

LDAK
Desktop

LDAK Linkage-Disequilibrium Adjusted Kinships

A software for computing LD-adjusted kinships. The original use of LDAK was to…

A software for computing LD-adjusted kinships. The original use of LDAK was to adjust for linkage disequilibrium (LD) by calculating SNP weightings which downweight the contribution of SNPs in highly…

Haploview
Desktop

Haploview

A comprehensive suite of tools for haplotype analysis for a wide variety of…

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…

LDheatmap
Desktop

LDheatmap

Produces a graphical display, as a heat map, of measures of pairwise linkage…

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…

MendelSoft
Desktop

MendelSoft

Detects marker genotyping incompatibilities according to their features.…

Detects marker genotyping incompatibilities according to their features. MendelSoft works about Mendelian errors only in situation of complex pedigrees. This tool operates with different data as…

LinkageTracker
Algorithm

LinkageTracker

Represents a highly accurate in both simulation-generated and real genetic…

Represents a highly accurate in both simulation-generated and real genetic datasets. LinkageTracker does not require any population ancestry information and allows for the disease mutation to occur…

Linkage…
Desktop

Linkage Disequilibrium with Several Options

Serves for the QTL detection. LDSO uses fine-mapping methods or studies about…

Serves for the QTL detection. LDSO uses fine-mapping methods or studies about genome-wide association to produce this QTL detection. This tool helps for studying the population histories. This study…

SNAP
Web

SNAP SNP Annotation and Proxy Search

Finds proxy SNPs based on linkage disequilibrium, physical distance and/or…

Finds proxy SNPs based on linkage disequilibrium, physical distance and/or membership in selected commercial genotyping arrays. Pair-wise linkage disequilibrium is pre-calculated based on phased…

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