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.

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.

SwiftLink – Parallel MCMC Linkage Analysis

SwiftLink

:: 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.

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

QTLMap 0.9.7 – Linkage Analysis software to map QTLs in Outbred Populations

QTLMap 0.9.7

:: DESCRIPTION

QTLMap is a software dedicated to the detection of QTL from experimental designs in outbred population.The statistical techniques used are linkage analysis (LA) and linkage disequilibrium linkage analysis (LDLA) using interval mapping. Different versions of the LA are proposed from a  quasi Maximum Likelihood approach to a fully linear (regression) model.

::DEVELOPER

the Animal Genetics Division at INRA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 QTLMap

:: MORE INFORMATION

Citation

Elsen JM, Filangi O, Gilbert H, Legarra A, Le Roy P, Moreno C.
QTLMap : a software for the detection of QTL in full and half sib families.
Proceedings of the EAAP Annual Meeting: 2009.

QUIKLINK 1.6 – Linkage Analyses with a Variety of Programs

QUIKLINK 1.6

:: DESCRIPTION

QUIKLINK is a program which facilitates setting up linkage analyses using MLINK, LINKMAP, ILINK, VITESSE and MFLINK. To a large extent it performs the same functions as the LCP program supplied with the LINKAGE programs and as DOLINK, although LCP and QUIKLINK can each do things which the other cannot. The main features of QUIKLINK are that it can be used to set up standard linkage analyses quickly and easily, that it can be used in batch mode as well as interactive mode, that it can set up analyses with VITESSE and with MFLINK and that it can be used to set up analyses to estimate marker allele frequencies with ILINK. However it cannot deal with the full range of locus types and analyses which can be handled by LCP and the LINKAGE programs.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

QUIKLINK

:: MORE INFORMATION

TABLE 1.9 – Convert Output from Linkage Analysis to more Readable Form

TABLE 1.9

:: DESCRIPTION

TABLE takes the output from MLINK or LINKMAP and tabulates it in a more easily digestible form. It can also produce files suitable for graphing lod scores and for input to HOMOG, BTEST and FASTMAP.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

TABLE

:: MORE INFORMATION

SIBLINK 3.0 – Multipoint Linkage Analysis

SIBLINK 3.0

:: DESCRIPTION

SIBLINK allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Solaris 7 (or higher)

:: DOWNLOAD

 SIBLINK

:: MORE INFORMATION

Citation

Shah SH, Schmidt MA, Mei H, Scott WK, Hauser ER, Schmidt S.
Searching for epistatic interactions in nuclear families using conditional linkage analysis.
BMC Genet. 2005 Dec 30;6 Suppl 1:S148.

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

Paed Lab @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  EcMap

:: MORE INFORMATION

QMFLINK 1.1 – Model-free Linkage Analysis of Quantitative Traits

QMFLINK 1.1

:: DESCRIPTION

QMFLINK is a program which automates setting up likelihood calculations for linkage analysis of a quantitative trait using a variety of different transmission models, and then collating the results in order to produce model free lod scores.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

QMFLINK

:: MORE INFORMATION

Citation:

J. Knight, B.V. North, P.C. Sham and D. Curtis (2003)
Mapping loci influencing blood pressure in the Framingham pedigrees using model-free lod score analysis of a quantitative trait.
BioMed Central Genetics