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http://mga.bionet.nsc.ru/soft/index.html

Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software)

Proper citation: PEDIGREEQUERY (RRID:SCR_009041) Copy   

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http://genapha.icapture.ubc.ca/PathTutorial/

Web application to investigate gene-gene interactions in genetic association studies designed to: 1. Interface your SNP data with biological information from several online bioinformatics databases. 2. Generate biologically plausible hypotheses for testing gene-gene interactions. 3. Select a subset of SNPs and conduct SNP-SNP interaction tests. 4. Store analysis results. 5. Explore analysis results through interactive plots and summary tables. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PATH (RRID:SCR_009042) Copy   

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http://galton.uchicago.edu/~mcpeek/software/dhsmap/

Software application for fine-mapping of qualitative traits by linkage disequilibrium. Given a set of marker haplotypes or genotypes from affected individuals, haplotypes or genotypes from appropriately selected controls, and a genetic map of the markers at which both sets of individuals are typed, DHSMAP estimates the location of the trait-associated variant by maximum likelihood or maximum quasi-likelihood. (entry from Genetic Analysis Software)

Proper citation: DHSMAP (RRID:SCR_009160) Copy   

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

Software application that is a faster version of SLINK (entry from Genetic Analysis Software)

Proper citation: FASTSLINK (RRID:SCR_008664) Copy   

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

A set of Java programs for genetic epidemiology analysis (entry from Genetic Analysis Software)

Proper citation: GENEPI.JAR (RRID:SCR_008782) Copy   

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http://ibi.zju.edu.cn/software/qtlnetwork

Software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines. (entry from Genetic Analysis Software). QTLNetwork-2.0 for mapping quantitative trait loci (QTL) with epistatic effects and QE interaction effects in DH, RI, BC, F2, IF2 and BxFy populations, and for graphical presentation of QTL mapping results.

Proper citation: QTLNetwork (RRID:SCR_009078) Copy   

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http://www.hsph.harvard.edu/faculty/alkes-price/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application using a method for combining SNP association and admixture association statistics to increase power in GWAS in admixed populations. (entry from Genetic Analysis Software)

Proper citation: MIXSCORE (RRID:SCR_009076) Copy   

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http://www.twin-research.ac.uk/WebPowQ/PowQ.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A user-friendly, graphical package for power evaluation and enhancement planning through variance component linkage analysis in a multipoint framework. (entry from Genetic Analysis Software)

Proper citation: POWQ (RRID:SCR_009077) Copy   

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http://www.cs.helsinki.fi/u/prastas/haplovisual/

Software application (entry from Genetic Analysis Software)

Proper citation: HAPLOVISUAL (RRID:SCR_009073) Copy   

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http://www.uni-bonn.de/~umt70e/becker.html

Software application for haplotype association analysis of unphased genotype data. It can be used both for population data (case-control) and nuclear family data. The program is optimized for haplotype frequency estimation with the EM-algorithm for many markers. FAMHAP provides a method which searches for potential genotyping errors and several tests for haplotype-based association analysis. Particular emphasis is on Monte-Carlo simulations, which are necessary in the context of haplotype association, where asymptotic theory often fails, and in the context of multiple testing problems. (entry from Genetic Analysis Software)

Proper citation: FAMHAP (RRID:SCR_009070) Copy   

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http://www.rni.helsinki.fi/~mjs/

Software application to select a trait-associated subset of markers among many candidates. The program is based on Bayesian modeling/estimation and it suits for both quantitative and qualitative traits. It can handle bi- and multiallelic markers as well as applied in situations where part of the marker genotypes may be missing. As an output of the program, one obtains posterior estimate of number and positions of trait-associated markers. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BAMA (RRID:SCR_009071) Copy   

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http://bioinformatics.ust.hk/SNPHarvester.html

Software tool for detecting epistatic interactions in genome-wide association studies (entry from Genetic Analysis Software)

Proper citation: SNPHARVESTER (RRID:SCR_008536) Copy   

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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   

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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   

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http://www.montpellier.inra.fr/URLB/

Software application employing multilocus genotypes to select or exclude populations as origins of individuals (Assignment and Migrants Detection). (entry from Genetic Analysis Software)

Proper citation: GENECLASS (RRID:SCR_009065) 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://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   

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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   

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http://www.statgen.org/main/index.php/Downloads/Downloads

Software application that aims to speed up the preparation of linkage data files passed on to the Alohomora software for data from the Affymetrix or Illumina assays. Chip2Spell gathers the information necessary to supplement the genotype data (such as the genetic map of the markers and the population-specific allele frequencies) from publicly available annoation files from Affymetrix and Illumina. The program formats the genotype data for input into the Alohomora program. (entry from Genetic Analysis Software)

Proper citation: CHIP2SPELL (RRID:SCR_009060) Copy   

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