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LINKAGE ANALYSIS PROGRAMS

ALLEGRO
*Description A faster version of GENEHUNTER (30-fold of increase of speed)
Authors Daniel F Gudbjartsson, Kristjan Jonasson, Augustine Kong, Mike Frigge (DeCode Genetics, Inc. Iceland). Send email to allegro@decode.is
References
  • Abstract
     
  • Gudbjartsson DF, Jonasson K, Frigge ML, Kong A. (2000). Allegro, a new computer program for multipoint linkage analysis. Nature Genetics, 25(1): 12-13.
     
Website http://www.decode.com/software/

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FASTLINK (FASTer version of LINKage)
Authors Cottingham, Gupta, Idury, Schaffer, Shriram. Collaborators for version 4: Ann Becker, Dan Geiger.
References
  • Cottingham RW, Idury RM, Schaffer AA. (1993). Fast sequential gentic linkage computation. Am J. Hum Genet, 53, 252-263.
     
  • Schaffer AA, Gupta SK, Shriram K, Cottingham RW. (1994). Avoiding recomputation in linkage analysis. Human Heredity, 44, 225-237.
     
  • online README (version 3.0P, June, 1997)
    online README (version 4.1P, June, 1999)
    online README.updates (version 4.1P, February, 2008)

     
  • Dwarkadas S, Schaffer AA, Cottingham RW Jr, Cox AL, Keleher P, Zwaenepoel W. (1994). Parallelization of general-linkage analysis problems. Human Heredity, 44(3): 127-41.
     
  • Gupta SK, Schaffer AA, Cox AL, Dwarkadas S, Zwaenepoel W. (1995). Integrating parallelization strategies for linkage analysis. Computational Biomedical Research, 28(2): 116-39.
     
  • Schaffer AA. (1996). Faster linkage analysis computations for pedigrees with loops or unused alleles. Human Heredity, 46(4): 226-35.
     
  • Becker A, Geiger D, Schaffer AA. (1998). Automatic selection of loop breakers for genetic linkage analysis. Human Heredity, 48(1): 49-60.
     
  • Becker A, Bar-Yehuda R, Geiger D. (1999). Random Algorithms for the Loop Cutset Problem. UAI 1999, 49-56.
     
  • Schaffer AA. Loops in FASTLINK
     
  • Schaffer AA. The mystery of (the) unknown
     
  • Schaffer AA. Pedigree traversal in FASTLINK
     
Website http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html

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GENEHUNTER
*Description Multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction.
Authors Leonid KruglyakMark DalyMary Pat Reeve-DalyEric Lander
References
Website http://www.broad.mit.edu/ftp/distribution/software/genehunter/

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GENEHUNTER-IMPRINTING
*Description GENEHUNTER-IMPRINTING is a modification of the GENEHUNTER software package (version 1.3). It allows performing parametric (LOD-score) analysis of traits caused by imprinted genes - that is, of traits showing a parent-of-origin effect.
Authors K. Strauch
References Strauch K, Fimmers R, Kurz T, Deichmann KA, Wienker TF, Baur MP. (2000). Parametric and nonparametric multipoint linkage analysis with imprinting and two-locus-trait models: application to mite sensitization. Am J Hum Genet 66, 1945-1957.
Website http://www.staff.uni-marburg.de/~strauchk/software.html

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HOMOG/HOMOGM
Authors Jurg Ott (Columbia Univ)
References
  • Ott J. (1986). Linkage probability and its approximate confidence interval under possible heterogeneity. Genet Epidemiol Suppl. Suppl 1, 251-7.
     
  • Online documentation
     
Website ftp://linkage.rockefeller.edu/software/homog

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LAMP
*Description LAMP uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees. It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.
Author Li M, Boehnke M, and Abecasis GR
References Li M, Boehnke M, and Abecasis GR (2005). Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal. Am J Hum Genet 76:934-949.
Website http://www.sph.umich.edu/csg/abecasis/LAMP/

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LINKAGE - general pedigrees
Authors Versions 5.1, 5.2: Mark Lathrop, J. Lalouel, C. Julier, Jurg Ott
Version 6.0: Alan Young, Daniel Weeks, Mark Lathrop
References
  • Lathrop GM, Lalouel JM, Julier C, Ott J. (1984). Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci U S A. 81 (11), 3443-3446.
     
  • Lathrop GM, Lalouel JM. (1984). Easy calculations of lod scores and genetic risks on small computers. Am J Hum Genet. 36 (2), 460-5.
     
  • Lathrop GM, Lalouel JM, White RL. (1986). Construction of human linkage maps: likelihood calculations for multilocus linkage analysis. Genet Epidemiol. 3 (1), 39-52.
     
  • Am Soc Hum Genet annual meeting 1995 (Young, Weeks, Lathrop, Am J Hum Genet suppl, 57(4), A206 (1995)).
     
  • Online user's guide (May 93)
     
  • Schaffer AA. See also: The mystery of (the) unknown
     
  • Schaffer AA. See also: Pedigree traversal in FASTLINK
     
Website ftp://linkage.rockefeller.edu/software/linkage

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LOKI
*Description Program for analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci.
Authors Simon C. Heath (Centre National de Genotypage)
References Heath SC. (1997). Markov Chain Segregation and Linkage Analysis for Oligogenic Models. Am J Human Genet, 61, 748-760.
Website http://www.stat.washington.edu/thompson/Genepi/Loki.shtml

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MERLIN (Multipoint Engine for Rapid Likelihood INference)
*Description Merlin carries out single-point and multipoint analyses of pedigree data, including IBD and kinship calculations, nonparametric and variance component linkage analyses, error detection and information content mapping. For multipoint analyses in dense maps, Merlin allows the user to impose constraints on the number of recombinants between consecutive markers. Merlin estimates haplotypes by finding the most likely path of gene flow or by sampling paths of gene flow at all markers jointly. It can also list all possible nonrecombinant haplotypes within short regions. Finally, Merlin provides swap-file support for handling very large numbers of markers as well as gene-dropping simulations for estimating empirical significance levels.
Authors Goncalo Abecasis
References Abecasis GR, Cherny SS, Cookson WO and Cardon LR (2002). Merlin-rapid Analysis of Dense Genetic Maps Using Sparse Gene Flow Trees. Nature Genetics, 30, 97-101.
Website http://www.sph.umich.edu/csg/abecasis/Merlin

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OSA (Ordered Subset Analysis)
*Description OSA allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.
Authors William Duren, Mike Boehnke, Elizabeth Hauser
References
  • Hauser ER, Bass MP, Martin ER, Watanabe RM, Duren WL, Boehnke M. (2001). Power of the Ordered Subset Method for Detection and Localization of Genes in Linkage Analysis of Complex Traits. Am J Hum Genet, suppl 69:529.
     
  • Hauser ER, Watanabe RM, Duren WL, Bass MP, Langefeld CD, Boehnke M. (2004). Ordered subset analysis in genetic linkage mapping of complex traits. Genet Epidemiol. 27 (1), 53-63.
     
Website http://www.chg.duke.edu/research/osa.html

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S.A.G.E.
*Description The S.A.G.E. software provides researchers with the tools necessary for various types of statistical genetic analysis of human family data.
Authors R. Elston, J. Bailey-Wilson, G. Bonney, L. Tran, B. Keats, A. Wilson
Website http://darwin.cwru.edu/sage/

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SOLAR (Sequential Oligogenic Linkage Analysis Routines)
*Description SOLAR is a flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening.
Authors John Blangero, Kenneth Lange, Tom Dyer, Laura Almasy, Harald G?ing, Jeff Williams, and Charles Peterson
References
  • Almasy L, Blangero J (1998) Multipoint quantitative trait linkage analysis in general pedigrees. Am J Hum Genet 62:1198-1211.
     
  • Almasy L, Dyer TD, Blangero J (1997) Bivariate quantitative trait linkage analysis: Pleiotropy versus co-incident linkages. Genet Epidemiol 14:953-958.
     
  • Williams JT, Van Eerdewegh P, Almasy L, Blangero J (1999) Joint Multipoint Linkage Analysis of Multivariate Qualitative and Quantitative Traits. I. Likelihood Formulation and Simulation Results. Am J Hum Genet 65:1134-1147.
     
  • Blangero J, Almasy L (1997) Multipoint oligogenic linkage analysis of quantitative traits. Genet Epidemiol 14:959-964.
     
  • Mitchell BD, Ghosh S, Schneider JL, Birznieks G, Blangero J (1997) Power of variance component linkage analysis to detect epistasis. Genet Epidemiol 14:1017-1022.
     
  • Williams JT, Blangero J (1999) Power of variance component linkage analysis to detect quantitative trait loci. Ann Hum Genet 63(6):545-563.
     
  • Williams JT, Blangero J (1999) Comparison of variance components and sibpair-based approaches to quantitative trait linkage analysis in unselected samples. Genet Epidemiol 16(2):113-134.
     
  • SOLAR user? guide
     
?. and more. Please refer the following website for more references.
Website http://solar.sfbrgenetics.org/

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SUPERLINK
*Description The program performs exact linkage analysis with the same input-output relationships as in standard genetic linkage programs such as LINKAGE, FASTLINK, VITESSE, but can run larger files than previous programs.
Authors Ma'ayan Fishelson
References Fishelson M, Geiger D. (2002). Exact genetic linkage computations for general pedigrees. Bioinformatics, 18(suppl 1), S189-S198.
Website http://bioinfo.cs.technion.ac.il/superlink/

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VITESSE
*Description Calculates likelihood on pedigrees
Authors Jeff O'Connell
References
  • O'Connell, Weeks. (1995). Am J Hum Genet, suppl 57, A199.
     
  • O'Connell, Weeks. (1995). Nature Genetics, 11, 402-408.
     
  • Online ReadMe file
     
Website http://watson.hgen.pitt.edu/register/soft_doc.html

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* Description retrieved from http://linkage.rockefeller.edu/soft/