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http://ib.berkeley.edu/labs/slatkin/eriq/software/mdb_web/

Software application using the mimimum description length model to delineate haplotype blocks (entry from Genetic Analysis Software)

Proper citation: MDBLOCKS (RRID:SCR_009280) Copy   

•   Source: SciCrunch Registry

http://www.biostat.umn.edu/~nali/SoftwareListing.html

Software application that implements the PAC (Products of Approximate Conditional) model for estimating recombination rate (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HOTSPOTTER (RRID:SCR_009238) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/h-1.html#homoghomogm

Software application (entry from Genetic Analysis Software)

Proper citation: HOMOG/HOMOGM (RRID:SCR_009237) Copy   

•   Source: SciCrunch Registry

http://l.web.umkc.edu/liujian/

Software platform that is based on real haplotype data from the HapMap ENCODE project that can simulate heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model. Moreover, both qualitative and quantitative traits can be simulated using additive genetic model with various genetic parameters designated by users. (entry from Genetic Analysis Software)

Proper citation: HAPSIMU (RRID:SCR_009235) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/Haplo/docMain.htm

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOTYPER (RRID:SCR_009232) Copy   

•   Source: SciCrunch Registry

http://www-genepi.med.utah.edu/Genie/

Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GENIE (RRID:SCR_009197) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/~mfarrall/twoloc.htm

Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software)

Proper citation: TWOLOC (RRID:SCR_009230) Copy   

•   Source: SciCrunch Registry

http://pngu.mgh.harvard.edu/~purcell/gpc/

Software application for automated power analysis for variance components (VC) quantitative trait locis (QTL) linkage and association tests in sibships, and other common tests (entry from Genetic Analysis Software)

Proper citation: GENETIC POWER CALCULATOR (RRID:SCR_009198) Copy   

•   Source: SciCrunch Registry

http://www.daimi.au.dk/~mailund/GeneRecon/

Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software)

Proper citation: GENERECON (RRID:SCR_009195) Copy   

•   Source: SciCrunch Registry

http://www.chem.agilent.com/scripts/pds.asp?lpage=34662

A desktop analysis workbench for analyzing high-volume, high-density genotyping data. The software provides a comprehensive set of linkage and association algorithms that allow researchers to discover relationships between genotypes and phenotypes. Researchers can visually explore fully annotated SNPs and genes at varying levels of detail. Designed for biologists and statisticians, GeneSpring GT is capable of importing, visualizing, and analyzing hundreds of thousands of variation measurements simultaneously, for rapid localization of disease or phenotype markers. (entry from Genetic Analysis Software)

Proper citation: GENESPRING GT (RRID:SCR_009196) Copy   

•   Source: SciCrunch Registry

http://www.broad.mit.edu/ftp/distribution/software/genehunter/

Software application for multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER (RRID:SCR_009191) Copy   

•   Source: SciCrunch Registry

https://www.helmholtz-muenchen.de/en/ige/service/software-download/genehunter-imprinting/index.html

Software application that is a modification of the GENEHUNTER software package (version 1.3)that allows users to perform parametric (LOD-score) analysis of traits caused by imprinted genes - that is, of traits showing a parent-of-origin effect. (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-IMPRINTING (RRID:SCR_009192) Copy   

•   Source: SciCrunch Registry

http://info.med.yale.edu/genetics/kkidd/programs.html

A simple software program for graphical presentation of haplotype block structures, tagSNP selection and SNP variation. (entry from Genetic Analysis Software)

Proper citation: HAPLOT (RRID:SCR_009228) Copy   

•   Source: SciCrunch Registry

http://bioinfo.cs.technion.ac.il/haploblock/

Software package which provides an integrated approach to haplotype block identification, haplotype resolution and linkage disequilibrium mapping, suitable for high-density phased or unphased SNP data. (entry from Genetic Analysis Software)

Proper citation: HAPLOBLOCK (RRID:SCR_009223) Copy   

•   Source: SciCrunch Registry

http://snp.bumc.bu.edu/modules.php?name=HaploBuild

Software application for constructing and testing haplotypes for SNPs in close physical proximity to one another but which are not necessarily contiguous. Furthermore, the number of SNPs contained in the haplotype is not restricted, thereby permitting the evaluation of complex haplotype structures. The analysis of large amounts of SNP data creates difficulties for the analysis of haplotypes and their association to traits of interest. Commonly fairly simple methods, such as two- or three-SNP sliding windows are used to create haplotypes across large regions, but these may be of limited value when adjacent SNPs are in strong LD and provide redundant information. This program alleviates these difficulties. (entry from Genetic Analysis Software)

Proper citation: HAPLOBUILD (RRID:SCR_009224) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/~marchini/software/gwas/hapgen.html

Software application that simulates case control datasets at SNP markers and can output data in the FILE FORMAT used by IMPUTE, SNPTEST and GTOOL. The approach can handle markers in LD and can simulate datasets over large regions such as whole chromosomes. Hapgen simulates haplotypes by conditioning on a set of population haplotypes and an estimate of the fine-scale recombination rate across the region. The disease model is specified through the choice of a single SNP as the disease causing variant together with the relative risks of the genotypes at the disease SNP. The program is designed to work with publically available files that contain the haplotypes estimated as part of the HapMap project and the estimated fine-scale recombination map derived from that data. Hapgen is computationally tractable. On a modern desktop HAPGEN can simulate several thousand case and control data on a whole chromosome at Hapmap Phase 2 marker density within minutes. This program has been used to assess the power of several different commercially available genotyping chips, in the design stage of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC) and for evaluating the power of different methods for detecting association in genome-wide studies. (entry from Genetic Analysis Software)

Proper citation: HAPGEN (RRID:SCR_009221) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/HAPINFERX.md

Software application (entry from Genetic Analysis Software)

Proper citation: HAPINFERX (RRID:SCR_009222) Copy   

•   Source: SciCrunch Registry

http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php

Software application designed to accompany the second edition of Bruce Weir''s book Genetic Data Analysis (1996. Sinauer Associates) (entry from Genetic Analysis Software)

Proper citation: GDA (RRID:SCR_009187) Copy   

•   Source: SciCrunch Registry

http://www-hto.usc.edu/msms/HapBlock/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPBLOCK (RRID:SCR_009220) Copy   

•   Source: SciCrunch Registry

http://users.ox.ac.uk/~ayoung/gas.html .

Software application for statistical analysis of genetic linkage data, sib-pair analysis, association studies (entry from Genetic Analysis Software)

Proper citation: GAS (RRID:SCR_009184) Copy   

•   Source: SciCrunch Registry