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http://www.stat.washington.edu/thompson/Genepi/Hardy.shtml

Markov chain Monte Carlo program for association in two-dimensional contingency tables, and for testing Hardy-Weinberg equilibrium. (entry from Genetic Analysis Software)

Proper citation: HARDY (RRID:SCR_009107) Copy   

•   Source: SciCrunch Registry

http://www.biostat.harvard.edu/~clange/default.htm

An interactive software package that provides tools for the design and the data analysis of family-based association studies. (entry from Genetic Analysis Software)

Proper citation: PBAT (RRID:SCR_009105) Copy   

•   Source: SciCrunch Registry

http://www.statistics.com/software-directory/helixtree

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

Proper citation: HELIXTREE (RRID:SCR_009067) Copy   

•   Source: SciCrunch Registry

http://www.molecular-haplotype.org/finesse/finesse_intro.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application to incorporate regressive models into the VITESSE likelihood engine.

Proper citation: FINESSE (RRID:SCR_009100) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016.

Proper citation: SVCC (RRID:SCR_009068) 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   

•   Source: SciCrunch Registry

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://embio.yonsei.ac.kr/haplowser/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOWSER (RRID:SCR_009095) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles.

Proper citation: MOSCPHASER (RRID:SCR_009092) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/UMAKE

Software pipeline to detect SNPs and call their genotypes from a list of BAM files. UMAKE pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies. (entry from Genetic Analysis Software)

Proper citation: UMAKE (RRID:SCR_009093) Copy   

•   Source: SciCrunch Registry

http://www.cnrs-gif.fr/pge/bioinfo/lea/index.php?lang=en

Software application (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LEA (RRID:SCR_009090) 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   

•   Source: SciCrunch Registry

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.sanger.ac.uk/resources/software/ariel/

Software application that explores the effects of rare variants within complex traits through locus-based analysis. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, ARIEL has been developed as a locus-wide regression-based collapsing approach that incorporates variant quality scores. (entry from Genetic Analysis Software)

Proper citation: ARIEL (RRID:SCR_009126) Copy   

•   Source: SciCrunch Registry

http://dmpi.duke.edu/apl-osa-beta-version

Software application that in the presence of genetic heterogeneity, can identify a genetically homogenous subset of families based on a trait-related covariate. APL-OSA then tests the relationship between the association statistics (i.e., the APL statistics) calculated based on the subset and the family-specific covariate. APL-OSA is based on the OSA method for linkage and the family-based association test, APL. Thus, APL-OSA has similar properties with OSA and APL. Bi-alleleic markers such as SNPs are accepted by APL-OSA. APL-OSA is a single-marker test and considers one covariate each time. (entry from Genetic Analysis Software)

Proper citation: APL-OSA (RRID:SCR_009124) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/soft_doc.html registration page at: http://watson.hgen.pitt.edu/register

Software application (entry from Genetic Analysis Software)

Proper citation: APM (RRID:SCR_009125) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/soft_doc.html,

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that calculates likelihood on pedigrees (entry from Genetic Analysis Software)

Proper citation: VITESSE (RRID:SCR_009089) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that extends partially observed genotype data to the whole pedigree. Can be used for generating starting points for MCMC samplers and for checking that the genotype data are consistent with the pedigree structure.

Proper citation: APE (RRID:SCR_009122) Copy   

•   Source: SciCrunch Registry