Tag: Linkage Analysis

SLINK 3.02 – Simulation program for Linkage Analysis

SLINK 3.02

:: DESCRIPTION

The program SLINK is a general computer simulation program that employs a variation of the algorithm described by Ott (1989).  Suppose there are N people in a pedigree.  Let x = (x1,x2,…,xN) represent the vector of phenotypes of the N people in the pedigree.  Likewise, let g = (g1, g2,…,gN) represent the vector of multi-locus genotypes including phase information.

::DEVELOPER

Division of Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C++ Compiler
  • LINKAGE

:: DOWNLOAD

  SLINK

:: MORE INFORMATION

Citation:

Hum Hered. 2011;71(2):126-34. doi: 10.1159/000324177. Epub 2011 Jul 6.
Coordinated conditional simulation with SLINK and SUP of many markers linked or associated to a trait in large pedigrees.
Schäffer AA1, Lemire M, Ott J, Lathrop GM, Weeks DE.

Weeks DE, Ott J, Lathrop GM (1990)
SLINK: a general simulation program for linkage analysis.
Am J Hum Genet 47:A204

SwiftLink 2.0 – Parallel MCMC Linkage Analysis

SwiftLink 2.0

:: DESCRIPTION

SwiftLink performs multipoint parametric linkage analysis on large consanguineous pedigrees and is primarily targeted at pedigrees that cannot be analysed by a Lander-Green algorithm based program, i.e. many markers, but larger pedigrees.

::DEVELOPER

SwiftLink team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SwiftLink

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Feb 15;29(4):413-9. doi: 10.1093/bioinformatics/bts704. Epub 2012 Dec 13.
SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU.
Medlar A1, Głowacka D, Stanescu H, Bryson K, Kleta R.

GADS 1.1 – Parametric Linkage Analysis of Quantitative Traits

GADS 1.1

:: DESCRIPTION

GADS is aoftware for Genetic Analyses of quantitative traits Distributed with Spike on the base of large pedigrees without loops

::DEVELOPER

Group of the Methods of Genetic Analysis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Perl
  • Python

:: DOWNLOAD

 GADS

:: MORE INFORMATION

Citation:

GADS software for parametric linkage analysis of quantitative traits distributed as a point-mass mixture.
Axenovich TI, Zorkoltseva IV.
Comput Biol Chem. 2012 Feb;36:13-4. doi: 10.1016/j.compbiolchem.2011.11.004.

PedCut 1.19 – Cutting large and complex Pedigrees for Linkage Analysis

PedCut 1.19

:: DESCRIPTION

PedCut is a program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size

::DEVELOPER

Group of the Methods of Genetic Analysis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PedCut

:: MORE INFORMATION

Citation:

Eur J Hum Genet. 2008 Jul;16(7):854-60. doi: 10.1038/ejhg.2008.24. Epub 2008 Feb 27.
An approach for cutting large and complex pedigrees for linkage analysis.
Liu F, Kirichenko A, Axenovich TI, van Duijn CM, Aulchenko YS.

BestRepeat 1.0 – Variance Components Linkage Analysis with Repeated Measurements

BestRepeat 1.0

:: DESCRIPTION

BestRepeat is a R package to calculate the optimal number of repeated measures for quantitative trait linkage analysis.

::DEVELOPER

Liming Liang

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BestRepeat

:: MORE INFORMATION

Citation

Liang L, Chen WM, Sham PC and Abecasis GR. (2009)
Variance Components Linkage Analysis with Repeated Measurements.
Human Heredity 67: 237-247.

EcMap – Evaluate the size of Families for Linkage analysis

EcMap

:: DESCRIPTION

EcMap is a simulation program that allows users to evaluate the size of their families for linkage analysis. The software simulates homologous recombination and inheritance process based on a Chi-square model simulating physical interference but not chromatid interference. The genetic distance map was obtained from HapMap and reflects average male and female genetic distances for each chromosome

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  EcMap

:: MORE INFORMATION

power.HE 1.2 – Calculate Sample Size and Power for the Haseman-Elston method in Linkage Analysis

power.HE 1.2

:: DESCRIPTION

power.HE is designed to calculate sample size and power for the Haseman-Elston method in linkage analysis for a quantitative trait.

::DEVELOPER

Institute of Medical Biometry and Statistics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Window/ MacOsX
  • R package

:: DOWNLOAD

 power.HE

:: MORE INFORMATION

SASGene 1.2 – Gene Segregation and Linkage analysis in Breeding Population

SASGene 1.2

:: DESCRIPTION

SASGene is a SAS computer program for gene segregation and linkage analysis in breeding population

::DEVELOPER

Cucurbit Breeding at NC State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SASGene

:: MORE INFORMATION

Citation

Liu, J. S., T. C. Wehner, and S. B. Donaghy. 1997.
SASGene: A SAS computer program for genetic analysis of gene segregation and linkage.
J. Hered. 88: 253-254.

LINKMFEX 2.4 – LINKage analysis package for outcrossed families with Male Female EXchange of the mapping parent

LINKMFEX 2.4

:: DESCRIPTION

LINKMFEX is a set of programs will allow you to analyze the segregation results from pairwise sets of loci in outbred families for possible linkage relationships. The same input data file may be used to analyze linkage relationships among loci using either parent as the mapping parent.

::DEVELOPER

Roy G. Danzmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LINKMFEX

:: MORE INFORMATION

Pelican 1.2.1 – Pedigree Editor for LInkage Computer ANalysis

Pelican 1.2.1

:: DESCRIPTION

Pelican is a Pedigree Editor for LInkage Computer ANalysis. It is a utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file.

::DEVELOPER

Frank Dudbridge

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 Pelican

:: MORE INFORMATION

Citation

F Dudbridge, T Carver, GW Williams (2004),
“Pelican: pedigree editor for linkage computer analysis“,
Bioinformatics, 20(14):2327-2328.