Tag: Two-Locus

TLINKAGE 20 – Two-locus Linkage Analysis

TLINKAGE 20

:: DESCRIPTION

The Tlinkage programs described here are an extension of the general LINKAGE programs for genetic linkage analysis. The extension consists of allowing for a disease phenotype to be under the control of two loci. The current version (20 Apr 2007) corrected a bug that had an effect only with relatively large numbers of alleles at the marker loci.

::DEVELOPER

Jurg Ott, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 TLINKAGE

:: MORE INFORMATION

Citation

Schork NJ, Boehnke M, Terwilliger JD, Ott J (1993)
Two trait locus linkage analysis: a powerful strategy for mapping complex genetic traits.
Am J Hum Genet 53, 1127-1136

EPIBLASTER 1.0 – Two-locus Epistasis Detection Strategy using GPU

EPIBLASTER 1.0

:: DESCRIPTION

The purpose of EPIBLASTER is to compute the differences of correlation coefficients between Controls and Cases as a mean to isolate for significant SNPs Interactions using gpuCor function of the gputools package on a CUDA enabled graphic card

::DEVELOPER

Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package
  • gputools R package
  • CUDA developer driver and Toolkit
  • GENABLE

:: DOWNLOAD

 EPIBLASTER

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2011 Apr;19(4):465-71. doi: 10.1038/ejhg.2010.196.
EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units.
Kam-Thong T, Czamara D, Tsuda K, Borgwardt K, Lewis CM, Erhardt-Lehmann A, Hemmer B, Rieckmann P, Daake M, Weber F, Wolf C, Ziegler A, Pütz B, Holsboer F, Sch?lkopf B, Müller-Myhsok B.

SNPAssociation – Detecting Two-locus Associations allowing for Interactions in GWAS

SNPAssociation

:: DESCRIPTION

SNPAssociation is a code for testing associations allowing for interactions in genome-wide association studies.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SNPAssociation

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Oct 15;26(20):2517-25. doi: 10.1093/bioinformatics/btq486. Epub 2010 Aug 24.
Detecting two-locus associations allowing for interactions in genome-wide association studies.
Wan X1, Yang C, Yang Q, Xue H, Tang NL, Yu W.

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.

TWOLOC – Analyze Two-locus Susceptibility Gene Models in affected Sib-pair data

TWOLOC

:: DESCRIPTION

TWOLOC is a software package for analyzing two-locus susceptibility gene models in affected sib-pair data

::DEVELOPER

Professor Martin Farrall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TWOLOC

:: MORE INFORMATION

Citation:

Farrall M ,
Affected sibpair linkage tests for multiple linked susceptibility genes,
Genetic Epidemiology 1997; 14:103-115.

TEAM 0.0.4 – Two-locus Epistasis tests in human Genome-wide Association Study

TEAM 0.0.4

:: DESCRIPTION

TEAM is a software significantly speeds up epistasis detection for human GWAS.

::DEVELOPER

the UNC Computational Genetics Working Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 TEAM

:: MORE INFORMATION

Citation

Xiang Zhang, Shunping Huang, Fei Zou and Wei Wang
TEAM: Efficient Two-Locus Epistasis Tests in Human Genome-Wide Association Study
Bioinformatics (2010) 26 (12): i217-i227.

COE 0.0.5 – Genome-Wide Two-Locus Epistasis Test in Disease Association Study

COE 0.0.5

:: DESCRIPTION

COE is a software for efficient large scale gene-gene interaction analysis, which supports a wide range of tests.

::DEVELOPER

the UNC Computational Genetics Working Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 COE 

:: MORE INFORMATION

Citation

Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, and Wei Wang.
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study
Journal of Computational Biology. March 2010, 17(3): 401-415. doi:10.1089/cmb.2009.0155.

EPISTACY 2.0 – Detect Two-locus Epistatic Interactions using Genetic Marker information

EPISTACY 2.0

:: DESCRIPTION

EPISTACY is a SAS program designed to test all possible two-locus combinations for epistatic (interaction) effects on a quantitative trait using QTL-mapping data sets.

::DEVELOPER

Dr Jim Holland 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 EPISTACY

:: MORE INFORMATION

Citation

Holland (1998),
“EPISTACY: A SAS program for detecting two-locus epistatic interactions using genetic marker information“,
Journal of Heredity, 89:374-375.

ASF – Two-Locus Asymptotic Sampling Formula

ASF

:: DESCRIPTION

ASF (Asymptotic Sampling Formula) is a software that computes the first three terms for either the infinite-alleles model or the finite-alleles PIM model.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

  ASF

:: MORE INFORMATION

Citation

Jenkins, P.A. and Song, Y.S.
Closed-form two-locus sampling distributions: accuracy and universality
Genetics, 183 (2009) 1087-1103.”