Tag: LD

Haploview 4.2 – Analysis & Visualization of LD & Haplotype Maps

Haploview 4.2

:: DESCRIPTION

Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.

::DEVELOPER

The Analytic and Translational Genetics Unit(AUGT)，The Broad Institute,

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Haploview

:: MORE INFORMATION

Citation

Barrett JC, Fry B, Maller J, Daly MJ.
Haploview: analysis and visualization of LD and haplotype maps.
Bioinformatics. 2005 Jan 15 [PubMed ID: 15297300]

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.

2LD / LDSHELL – Two-locus LD Calculator and Shell

2LD / LDSHELL

:: DESCRIPTION

2LD is a simple program calculating linkage disequilibrium (LD) measures between two polymorphic markers.

LDSHELL is a shell program for 2LD

::DEVELOPER

Jing Hua Zhao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux/Windows/

:: DOWNLOAD

 2LD , LDSHELL

:: MORE INFORMATION

Citation

Zhao, J. H. (2004)
“2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis“.
Bioinformatics, 20, 1325-1326

Noonan, J.P., Li, J., Nguyen, L., Caolie, C., Dickson, M., Grimwood, J., Schmutz, J., Feldman, M. W., Myers, R. M. (2003),
Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster
Am. J. Hum. Genet.Vol. 72, pp. 621-635.