MC-PDT 0.2.4 – Linkage Disequilibrium Test

MC-PDT 0.2.4

:: DESCRIPTION

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.

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MC-PDT

:: MORE INFORMATION

Citation

Jie Ding, Shili Lin, Yang Liu (2006).
Monte Carlo Pedigree Disequilibrium Test for Markers on X Chromosome.
American Journal of Human Genetics, 79, 567-573.

ALDER 1.03 – Compute Weighted Linkage Disequilibrium (LD) Curves

ALDER 1.03

:: DESCRIPTION

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.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ALDER

:: MORE INFORMATION

Citation

Loh P-R, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, and Berger B.
Inference of Admixture Parameters in Human Populations Using Weighted Linkage Disequilibrium.

GOLD 1.1.0 – Graphical Overview of Linkage Disequilibrium

GOLD 1.1.0

:: DESCRIPTION

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.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

GOLD

:: MORE INFORMATION

If you decide to use GOLD, please take a minute to register.

QTDT 2.6.1 – Linkage Disequilibrium Analysis for Quantitative and Discrete Traits

QTDT 2.6.1

:: DESCRIPTION

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.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

QTDT

:: MORE INFORMATION

Citation:

Abecasis GR, Cardon LR and Cookson WO
A General Test of Association for Quantitative Traits in Nuclear Families.
Am J Hum Genet (2000) 66:279-292

Abecasis GR, Cookson WO and Cardon LR
Pedigree tests of transmission disequilibrium.
Eur J Hum Genet (2000) 8:545-51

If you decide to use QTDT, please take a minute to register.

BALD 0.1.1 – Blockwise Approach using Linkage Disequilibrium

BALD 0.1.1

:: DESCRIPTION

BALD is the R package BALD implements/combines functions for Genome-Wide Association Studies including simulation of SNPs data, constrained hierarchical clustering using Linkage Disequilibrium (LD) measures, the Gap statistic to find the optimal number of clusters, and statistical regression models for SNP selection (Univariate, Lasso, Group Lasso, Elastic-Net).

::DEVELOPER

Laboratoire de Mathématiques et Modélisation d’Évry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 BALD

:: MORE INFORMATION

Citation

Performance of a blockwise approach in variable selection using linkage disequilibrium information.
Dehman A, Ambroise C, Neuvial P.
BMC Bioinformatics. 2015 May 8;16:148. doi: 10.1186/s12859-015-0556-6.

LD-Plus – Display of Single SNP Statistics in the Context of Linkage Disequilibrium and Haplotype Structures

LD-Plus

:: DESCRIPTION

LD-Plus is a data visualization application for the display of single SNP statistics in the context of linkage disequilibrium and haplotype structures. LD-Plus can display both continuous and categorical SNP statistics, and is designed to parse Haploview output to display both D’ and r2 LD plots, called or user-defined haplotype blocks, and haplotype frequencies. This web application will run Haploview and use the output to generate the plots.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Ruby

:: DOWNLOAD

 LD-Plus

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Feb 15;26(4):578-9. Epub 2010 Feb 3.
Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus.
Bush WS, Dudek SM, Ritchie MD.

BALD – Bayesian Analysis of Linkage Disequilibrium Differences

BALD

:: DESCRIPTION

BALD is a Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals.

::DEVELOPER

BALD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BALD

:: MORE INFORMATION

Citation

A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals.
Clark TG, Campino SG, Anastasi E, Auburn S, Teo YY, Small K, Rockett KA, Kwiatkowski DP, Holmes CC.
Bioinformatics. 2010 Aug 15;26(16):1999-2003. Epub 2010 Jun 16.

SIMLD 1.0 – Simulate Linkage Disequilibrium

SIMLD 1.0

:: DESCRIPTION

SIMLD is a software package to simulate realistic linkage disequilibrium patterns based on HapMap data

::DEVELOPER

Xiguo Yuan 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SIMLD

:: MORE INFORMATION

Citation

Biochem Genet. 2011 Jun;49(5-6):395-409. doi: 10.1007/s10528-011-9416-x. Epub 2011 Jan 14.
Simulating linkage disequilibrium structures in a human population for SNP association studies.
Yuan X1, Zhang J, Wang Y.

snp.plotter 0.5.1 – SNP/haplotype Association and Linkage Disequilibrium plotting package

snp.plotter 0.5.1

:: DESCRIPTION

snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values.

::DEVELOPER

Augustin Luna, Kristin Nicodemus (email: augustin@mail.nih.gov)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 snp.plotter

:: MORE INFORMATION

Citation

Luna, Nicodemus (2007),
snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package“,
Bioinformatics, 23(6):774-776.

Overall LD – Assess the Overall Linkage Disequilibrium

Overall LD

:: DESCRIPTION

Overall LD is a program to assess the overall Linkage Disequilibrium (LD) over several markers and assess the LD between groups of markers.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Overall LD

:: MORE INFORMATION

Citation

Ann Hum Genet. 1999 Mar;63(Pt 2):167-79.
Assessing linkage disequilibrium in a complex genetic system. I. Overall deviation from random association.
Zhao H, Pakstis AJ, Kidd JR, Kidd KK.