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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   

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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   

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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   

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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   

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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   

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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   

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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   

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

Software application (entry from Genetic Analysis Software)

Proper citation: HAPBLOCK (RRID:SCR_009220) Copy   

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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

http://gump.qimr.edu.au/GAIA/gaia.html

Web-based application for testing for locus-locus interaction using genetic association. It is based upon the case-control study design and is designed so that non-specialists may routinely apply tests for interaction. GAIA allows simple testing of both additive and additive plus dominance interaction models and includes permutation testing to appropriately correct for multiple testing. The application is useful for both candidate gene based studies and genome-wide association studies. For large scale studies GAIA includes a screening approach which prioritizes loci for further interaction analysis. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GAIA (RRID:SCR_009182) Copy   

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http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for demonstration of method for preliminary ordering of loci based on two-point lod scores. (entry from Genetic Analysis Software)

Proper citation: FIRSTORD (RRID:SCR_009180) Copy   

•   Source: SciCrunch Registry

http://www.biomath.medsch.ucla.edu/faculty/klange/software.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 1st, 2022. Software application for genetic analysis of classical biometric traits like blood pressure or height that are caused by a combination of polygenic inheritance and complex environmental forces. (entry from Genetic Analysis Software)

Proper citation: FISHER (RRID:SCR_009181) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/l-1.html#loginserm_estihaplo

Software application (entry from Genetic Analysis Software)

Proper citation: LOGINSERM ESTIHAPLO (RRID:SCR_009258) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/multimap/

Software application for conversion of LINKAGE format data files to CRI-MAP format (entry from Genetic Analysis Software)

Proper citation: LNKTOCRI (RRID:SCR_009256) Copy   

•   Source: SciCrunch Registry

http://www.ktl.fi/molbio/software/linkbase/index.html

An easy and practical database-program made for researchers who want to connect the genotype data produced by automatic sequencers ( ABI Prism 377 (Perkin Elmer) and ALF (Pharmacia) ) to linkage and sib-pair programs. (entry from Genetic Analysis Software)

Proper citation: LINKBASE (RRID:SCR_009254) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: LIPED (RRID:SCR_009255) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/staff/churchill/labsite/software/Jqtl/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A Java GUI for the popular QTL data analysis software R/QTL that provides a flexible and powerful working environment for users to perform a variety of tasks. (entry from Genetic Analysis Software)

Proper citation: J/QTL (RRID:SCR_009250) Copy   

•   Source: SciCrunch Registry

http://balance.med.utah.edu/wiki/index.php/JPSGCS

Software application to address problems in statistical genetics; however, they include several programs and packages that may be more generally useful, for instance, programs to draw and manipulate graphs, simulation programs, and programs to estimate graphical models. (entry from Genetic Analysis Software)

Proper citation: JPSGCS (RRID:SCR_009249) Copy   

•   Source: SciCrunch Registry