Tag: Linkage Analysis

LIden – Linkage Analysis Software

LIden

:: DESCRIPTION

LIden determines allele sharing status among family members using high-density SNP data. It takes SNP genotype data, pedigree structure and physical-locus-file as input, and outputs allele sharing graphical display files and linked regions

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LIden

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jul 15;10:216.
Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference.
Wang L, Wang Z, Yang W.

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

LIPED – Program for Linkage Analysis

LIPED

:: DESCRIPTION

LIPED program (for LIkelihoods in PEDigrees) estimates the recombination fraction by calculating pedigree likelihoods for various assumed values of the recombination fraction. The algorithm is based on Elston and Stewart (1971) with some extensions. Its first application (to the large Alaska pedigree, Schrott et al. 1972) resulted in mild evidence for linkage of familial hypercholesterolemia to the C3 polymorphism (Ott et al 1974), which was later confirmed by various authors. This disease locus (LDLR, previously FH and FHC) is now located on chromosome 19p13.3

::DEVELOPER

Jurg Ott, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LIPED

:: MORE INFORMATION

Terwilliger JD, Ott J (1994) Handbook of Human Genetic Linkage. Johns Hopkins University Press, Baltimore

LINKAGE – Pedigree Linkage Analysis

LINKAGE

:: DESCRIPTION

LINKAGE package is a series of programs for maximum likelihood estimation of recombination rates, calculation of lod score tables, and analysis of genetic risks. The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. Programs in the second group are for three-generation families and codominant marker loci, and are primarily intended for the construction of genetic maps from data on reference families.

::DEVELOPER

Lab of Statistical Genetics, Rockefeller University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

 LINKAGE

:: MORE INFORMATION

CovIBD – Linkage Analysis of Affected Sibpairs

CovIBD

:: DESCRIPTION

CovIBD refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values.

::DEVELOPER

The Devlin lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CovIBD

:: MORE INFORMATION

Citation:

Devlin, B., Jones, B.L., Bacanu, S., Roeder, K.,
“Mixture Models for Linkage Analysis of Affected Sibling Pairs and Covariates,”
Genetic Epidemiology, 2002, 22(1):52-65.

LOCUSMAP 2.1 – Rapid Linkage Analysis and Map Construction of Loci

LOCUSMAP 2.1

:: DESCRIPTION

Locusmap is a computer package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. The current version offers linkage analysis between codominant loci, between dominant loci, between codominant loci and dominant loci, and between codominant and sex-influenced, sex-linked, and imprinted loci. Using genotypic data supplied by the user, Locusmap calculates two-point recombination frequencies and LOD scores and then identifies linkage groups and orders loci within each linkage group automatically. Locusmap checks for genotypic and pedigree errors, and fills in missing genotypes when possible.

::DEVELOPER

JOHN GARBE AND YANG DA , Department of Animal Science, University of Minnesota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 LOCUSMAP

:: 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.

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

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

QTLMap team 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