MULTIDISEQ – Multipoint Linkage Analysis software which allows Marker-Marker LD

MULTIDISEQ

:: DESCRIPTION

MULTIDISEQ is multipoint linkage analysis software which allows Marker-Marker LD.

::DEVELOPER

Joseph D. Terwilliger and Alejandro Schäffer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MULTIDISEQ

:: MORE INFORMATION

Citation:

T Hiekkalinna, L Peltonen1, JD Terwilliger (2003),
“MULTIDISEQ: Computer software for multipoint linkage analysis of complex traits allowing for marker-marker LD (Linkage Disequilibrium)”
American Journal of Human Genetics, suppl, 73

LOT 1.2 – Linkage Analysis of Ordinal Traits

LOT 1.2

:: DESCRIPTION

LOT (Linkage analysis of Ordinal Traits) is a software program that performs linkage analysis of ordinal traits for pedigree data. It implements a latent-variable proportional-odds logistic model that relates inheritance patterns to the distribution of the ordinal trait.

::DEVELOPER

The Collaborative Center for Statistics in Science (C2S2)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 LOT

:: MORE INFORMATION

Citation:

Zhang, M., Feng, R., Chen, X., Hu, B., and Zhang, H. (2008)
LOT: a Tool for Linkage Analysis of Ordinal Traits for Pedigree Data.
Bioinoformatics 24;1737-9.

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.

GeneFinder 1.2.7 – Linkage Analysis with a Variety of Extensions

GeneFinder 1.2.7

:: DESCRIPTION

GeneFinder is a software package for linkage analysis with a variety of extensions.  GeneFinder continues a standard linkage software such as MERLIN by providing a more reasonable gene location estimation and the corresponding confidence interval estimate. In addition, GeneFinder provides a variety of linkage extensions such as adjusting for covariate heterogeneity, joint analysis of two linked disease susceptibility loci, linkage conditional on a known locus, etc.

::DEVELOPER

Wei-Min Chen

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux  / Windows / MacOsX

:: DOWNLOAD

 GeneFinder

:: MORE INFORMATION

SPLINK 1.09 – Sib Pair Linkage analysis

SPLINK 1.09

:: DESCRIPTION

SPLINK (Sib Pair Linkage analysis) is a program for linkage analysis using affected sib pairs. It uses the method of maximum likelihood to estimate the probability that two affected sibs share 0, 1 or 2 autosomal marker haplotypes identically by descent (IBD). For marker haplotypes on the X-chromosome, IBD sharing of maternal haplotypes only is considered. Parental marker data need not be present (although, of course, they help) and neither IBD status or phase of marker haplotype need be known. When full parental data are not available, the uncertainty in assigning parental haplotypes may be reduced by including data on sibs who are either unaffected or of unknown affection status.  When all available data still permit ambiguity for parental haplotypes, the population haplotype frequencies become relevant, and these are estimated internally, again using the method of maximum likelihood.

::DEVELOPER

David Clayton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows
  • C Compiler

:: DOWNLOAD

 SPLINK

:: MORE INFORMATION

Citation

Holmans, P. and Clayton, D. (1995).
Efficiency of typing unaffected relatives in an affected sib-pair linkage study with single locus and multiple tightly-linked markers.
Am J Hum Genet 57:1221-1232.

FLOSS 1.4.1 – Ordered Subset linkage Analysis

FLOSS 1.4.1

:: DESCRIPTION

FLOSS (flexible ordered subset analysis) software package uses input and output files from the MERLIN linkage analysis package (Abecasis et al, 2002) to perform an ordered subset analysis using either nonparametric linkage analysis z-scores or linear allele sharing model LOD scores.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 FLOSS

:: MORE INFORMATION

Citation:

Browning, BL (2006)
FLOSS: Flexible ordered subsets analysis for linkage analysis of complex traits.
Bioinformatics 22(4):512-3.

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

COMPUTATIONAL GENETICS 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.

Alohomora 0.33 – Linkage Analysis tools and Affymetrix Mapping

Alohomora 0.33

:: DESCRIPTION

Alohomora was designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array

::DEVELOPER

The Gene Mapping Center (GMC)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 Alohomora

:: MORE INFORMATION

Citation:

Ruschendorf F, Nurnberg P.
ALOHOMORA: a tool for linkage analysis using 10K SNP array data.
Bioinformatics. 2005 May 1; 21(9): 2123-5.

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

Wei-Min Chen, Liming Liang, @ the Center for Statistical Genetics

:: 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.

XWXW – Linkage Analysis of Quantitative Traits

XWXW

:: DESCRIPTION

XWXW implements the Unified Haseman-Elston method for non-parametric linkage test with quantitative traits. It optimally utilizes the information from a sib-pair. It is uniformly more powerful than both the classical H-E method and the revistited H-E method. Program GENIBD from SAGE or GeneHunter2 is required for sib-pair ibd estimation.

::DEVELOPER

FBAT-Toolkit Team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux/ Sunsparc stations

:: DOWNLOAD

XWXW

:: MORE INFORMATION

References

Xu X, Palmer LJ, Horvath S, and Wei LJ.  Combining Multiple Phenotypic Traits Optimally for Detecting Linkage with Sib-pair Observations. (2001) Genet. Epidemiol.

Xu X., Weiss S. Xu X., Wei LJ. A unified Haseman-Elston regression method for testing linkage with quantitative trait (2000) Am. J. Hum. Genet. 67: 1025-8