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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   

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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   

•   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   

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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   

•   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

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   

•   Source: SciCrunch Registry

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://bioinfo.ebc.ee/download/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Robust haploblock border reliability estimation tool implemented for LD based haploblock detection method. The most important new features are bootstrapping and overlapping block borders. (entry from Genetic Analysis Software)

Proper citation: BOOSTRAPPER (RRID:SCR_009135) Copy   

•   Source: SciCrunch Registry

http://www.geneticepi.com/Research/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. A set of programs for calculations under different linkage disequilibrium (LD) distribution models (entry from Genetic Analysis Software)

Proper citation: BOOLD (RRID:SCR_009134) Copy   

•   Source: SciCrunch Registry

http://www.rockefeller.edu/biolad-db/

Software application that is a research bioinformatics system for inputting, validating, organizing, archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password protected BiolAD-DB SQL compliant server database. BiolAD-DB tools further provide functionalities for generating customized reports and views. (entry from Genetic Analysis Software)

Proper citation: BIOLAD-DB (RRID:SCR_009131) Copy   

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http://www.htbiology.com/software.php

Collection of data analysis tools and interrelated biomedical information in a single easy-to-use software package that includes a component-based software/data integration platform that can quickly transform fragmented enterprise legacy data and software into an integrated suite of tools and knowledge base to achieve maximal usability, interoperability, scalability, and extensibility. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BIOIDE (RRID:SCR_009130) Copy   

•   Source: SciCrunch Registry

http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/

Software applications including ASP, a power calculator for gene mapping using a sibpair design (concordant or discordant) and ASPSHARE, which complements ASP in that it allows rapid calculation of the expected ibd sharing at the trait locus, based upon the model parameters, and the incidence corresponding to the respective parameters. (entry from Genetic Analysis Software)

Proper citation: ASP/ASPSHARE (RRID:SCR_009128) Copy   

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http://stephenslab.uchicago.edu/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: BIMBAM (RRID:SCR_009129) Copy   

•   Source: SciCrunch Registry

http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: EHPLUS (RRID:SCR_009159) Copy   

•   Source: SciCrunch Registry

http://www.gene.ucl.ac.uk/public-files/packages/jattwood/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for detecting and displaying well-characterized meiotic breakpoints in human family data.

Proper citation: CROSSFIND (RRID:SCR_009157) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/crimappvm.shtml

Software application that is a parallel version of CRIMAP (entry from Genetic Analysis Software)

Proper citation: CRIMAP-PVM (RRID:SCR_009156) Copy   

•   Source: SciCrunch Registry

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

A simulation program that simulates and plots (in real time) ancestral recombination graphs. This is currently primarily a teaching/educational tool. (entry from Genetic Analysis Software)

Proper citation: CHROMOSEG (RRID:SCR_009152) Copy   

•   Source: SciCrunch Registry