HAPLOTYPING PROGRAMS

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DANDELION  
Description Haplotyping program by Carl Langefeld
Authors Carl Langefeld
Website http://www.wakehealth.edu/Research/Center-for-Public-Health-Genomics/Resources/Resources.htm

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EHP.R
*Description Estimation of Haplotype frequencies from Pooled DNA samples. This program provides variance estimates for haplotype frequency estimates, it allows several kinds of missing information in the genotype data, it also allows for combined genotype data of different pool sizes. This program can be used for testing haplotype-disease associations in case control studies by calculating the likelihood ratio test: 2 log(likelihood for cases) + 2 log(likelihood for controls) - 2 log(likelihood for case+controls).
Authors Yaning Yang (Rockefeller University)
References Yang Y, Zhang J, Hoh J, Matsuda F, Xu P, Lathrop M, Ott J. (2003). Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proceedings of National Academy of Sciences, 100(12), 7225-7230.
Website http://linkage.rockefeller.edu/yyang/resources.html

 

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HAPLOBLOCK
Description HaploBlock is a software program which provides an integrated approach to haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and linkage disequilibrium (LD) mapping (or genetic association studies). HaploBlock is suitable for high density haplotype or genotype SNP marker data and is based on a statistical model which takes account of recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain at its core. (Description retrieved from http://bioinfo.cs.technion.ac.il/haploblock/)
Authors Gideon Greenspan, Dan Geiger
References
  • Model-based Inference of Haplotype Block Variation, Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB 2003). Also to appear in Journal of Computational Biology, Volume 11, Number 2-3.
  • High Density Linkage Disequilibrium Mapping using Models of Haplotype Block Variation. Accepted for ISMB 2004 and to appear in Bioinformatics.
  • Instruction Manual
  • LD Mapping Supplement
Website http://bioinfo.cs.technion.ac.il/haploblock/

 

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HAPLORE (HAPLOtype REconstruction in pedigrees)
Description A Program for Haplotype Reconstruction in Pedigrees (Description retrieved from http://zhaocenter.org/software/)
Authors Hongyu Zhao (Yale)
Website http://zhaocenter.org/software/

 

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HAPLO.STAT Video
Description

The haplo.stats package is a suite of R routines for the analysis of indirectly measured haplotypes.

The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (because of unknown linkage phase of the genetic markers). The genetic markers are assumed to be codominant (that is, 1-to-1 correspondence between their genotypes and their phenotypes). (Software updated August 2015.) (Description retrieved from http://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software)

Authors Dan Schaid, Jason Sinnwell, Charles Rowland, David Tines (Mayo Clinic)
References
  • Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. (2002). Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70: 425-434.
  • Manual (PDF)
Website http://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software

 

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HAPLOVIEW Video
 
*Description Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.
Authors Barrett JC, Fry B, Maller J, Daly MJ
References Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005 Jan 15.
Website http://www.broad.mit.edu/mpg/haploview/index.php

 

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HTR (Haplotype Trend Regression)
*Description Haplotype Trend Regression Haplotype association mapping using unrelated individuals; "fixed" and "sliding" window analysis; overall tests and tests for individual haplotype effects.
Authors Dmitri Zaykin
References Zaykin DV, Westfall PH, Young SS, Karnoub MC, Wagner MJ, Ehm MG. (2002). Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Human Heredity, 53, 79-91.
Website http://statgen.ncsu.edu/zaykin/htr.html

 

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PHASE Video Demo
*Description This program implements a new statistical method for reconstructing haplotypes from population genotype data. v2: (1) the introduction of a new computational approach, resulting in much faster haplotype resolution. (2) the introduction of a new model that allows for recombination and decay of Linkage Disequilibrium (LD) with distance, which results in more accurate haplotype estimates. This model also allows the user to estimate recombination rates, and identify recombination hotspots from population genotype data. (3) the facility to perform a test for haplotype frequency differences between cases and controls. (4) more extensive output summarising the results.
Authors Matthew Stephens
References Stephens M, Smith NJ, Donnelly P. (2001). AJHG, 68, 978-989.
Website https://els.comotion.uw.edu/express_license_technologies/phase

 

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SIMCROSS/SIMWALK
*Description Programs for generating optimal haplotype configurations on general pedigrees using a likelihood-based approach to correctly take intermarker recombination fractions into account. simcross ignores untyped parts of the pedigree, and it uses simulated annealing. simwalk combines simulated annealing with random walk method.
Authors Eric Sobel (UCLA) (in collaboration with Kenneth Lange, Jeffrey O'Connell, and Daniel E. Weeks)
References
  • Weeks DE, Sobel E, O'Connell JR and Lange K. (1995). Computer programs for multilocus haplotyping of general pedigrees. Am J Hum Genet, 56, 1506-1507.
  • Sobel E, Lange K, O'Connell JR, Weeks DE. Genetic Mapping and DNA Sequencing, Vol. 81; The IMA Volumes in Mathematics and its Applications; eds Speed TP, Waterman MS. (Springer-Verlag, 1996), pages 49-63.
  • Sobel E, Lange K. (1996). Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics. Am J Hum Genet, 58, 1323-1337.
  • Sobel E, Sengul H, Weeks DE. (2001). Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees. Human Heredity, 52, 121-131.
  • Sobel E, Papp JC, Lange K. (2002). Detection and integration of genotyping errors in statistical genetics. American Journal of Human Genetics, 70, 496-508.
  • SIMWALK manual
Website http://www.genetics.ucla.edu/software/simwalk

 

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