LINKAGE ANALYSIS PROGRAMS

ALLEGRO
FASTLINK (FASTer version of LINKage)
GENEHUNTER
GENEHUNTER-IMPRINTING
HOMOG/HOMOGM
LAMP
LINKAGE - general pedigrees
LOKI
MERLIN (Multipoint Engine for Rapid Likelihood INference)
OSA (Ordered Subset Analysis)
S.A.G.E.
SOLAR (Sequential Oligogenic Linkage Analysis Routines)
SUPERLINK
VITESSE

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/

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 files (version 3.0P, december 95). 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

GENEHUNTER
*Description	Multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction.
Authors	Leonid Kruglyak, Mark Daly, Mary Pat Reeve-Daly, Eric Lander
References	Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES. (1996). Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 58(6), 1347-1363. Online documentation (2.0 beta) Documentation in pdf fprmat (2.0beta) Online instruction (1.1, from Falling Rain Genomics, Inc.) Abstract by Markianos KG, Kruglyak L, Eberle MA. - Faster Multipoint Linkage Analysis Through State Space Reduction
Website	http://www.broad.mit.edu/ftp/distribution/software/genehunter/

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

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

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/

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

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

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

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://wwwchg.duhs.duke.edu/software/osa.html

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/

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://www.sfbr.org/solar/

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/

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

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