Tag: Linkage Disequilibrium

CubeX – Calculation of Pairwise Linkage Disequilibrium using Exact Solution

CubeX

:: DESCRIPTION

CubeX calculates haplotype frequencies using the exact solution to the cubic equation rather than an iterative approach.

::DEVELOPER

Tom Gaunt’s group in the MRC IEU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Mac OsX / Windows
  • Python

:: DOWNLOAD

 CubeX

:: MORE INFORMATION

Citation:

Gaunt TR, Rodríguez S, Day IN.
Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool ‘CubeX’.
BMC Bioinformatics. 2007 Nov 2;8:428.

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.

LDSO 1.02 – Linkage Disequilibrium with Several Options

LDSO 1.02

:: DESCRIPTION

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.

::DEVELOPER

F. Ytournel(contact author)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • fortran/G95

:: DOWNLOAD

 LDSO

:: MORE INFORMATION

Citation

J Anim Breed Genet. 2012 Oct;129(5):417-21. doi: 10.1111/j.1439-0388.2011.00986.x. Epub 2012 Jan 23.
LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces.
Ytournel F, Teyssèdre S, Roldan D, Erbe M, Simianer H, Boichard D, Gilbert H, Druet T, Legarra A.

LD Select 1.13 – Patterns of Linkage Disequilibrium Analysis

LD Select 1.13

:: DESCRIPTION

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.

::DEVELOPER

Dr. Deborah Nickerson’s lab at the University of Washington

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Max OS X
  • Perl

:: DOWNLOAD

LD Select

:: MORE INFORMATION

Citation

Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. Selecting a maximally informative set of single-nucleotide polymorphisms for association analysis using linkage disequilibrium. Am J Hum Genet. 2004 Jan;74(1):106-20. Epub 2003 Dec 15.

DMLE 2.3 – Disease Mapping using Linkage disEquilibrium

DMLE 2.3

:: DESCRIPTION

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).

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Windows

:: DOWNLOAD

 DMLE

:: MORE INFORMATION

Citation

J. Reeve and B. Rannala. 2002.
DMLE+: Bayesian linkage disequilibrium gene mapping.
Bioinformatics 18: 894-895

BLink 3.0 – compute Linkage Disequilibrium based on a Bayesian estimate of D’

BLink 3.0

:: DESCRIPTION

BLink (Bayesian Linkage) is a software to compute linkage disequilibrium based on a bayesian estimate of D’

::DEVELOPER

Bios, University of GranadaGranada , Spain

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 BLink

:: MORE INFORMATION

Citation:

Sebastiani P.; Abad-Grau M.M.
“Bayesian estimates of Linkage Disequilibrium”
BMC Genetics, 8, 1-13, 2007

Trimhap 1.2 – Linkage Disequilibrium

Trimhap 1.2

:: DESCRIPTION

Trimhap is a Fortran software package that implements the linkage disequilibrium mapping techniques

::DEVELOPER

Charles J. MacLean

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Trimhap

:: MORE INFORMATION

Citation:

MacLean CJ, Martin RB, Sham PC, Wang H, Straub RE, and Kendler KS. (2000).
The trimmed-haplotype test for linkage disequilibrium
American Journal of Human Genetics (March 2000 issue, Volume 66, Number 3, 1062).