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http://ihg.gsf.de/cgi-bin/hw/hwa1.pl (testing part)

Software application that tests for deviation from Hardy-Weinberg equilibrium and tests for association in case controls studies; Plot genotype frequencies graphically using a de Finetti diagram. (entry from Genetic Analysis Software)

Proper citation: FINETTI (RRID:SCR_009179) Copy   

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http://www.biostat.harvard.edu/~fbat/fbat.htm

Software application that allows the user to test for association/linkage between disease phenotypes and haplotypes by utilizing family-based controls. The method extends the approach for testing described in Rabinowitz and Laird (2000) to handle multiple tightly linked markers. It is robust to population admixture, yet efficient in the sense that it utilizes data from families where phase cannot be completely resolved in all individuals by using weights, which are estimated from the sample. However, the method remains robust to population stratification and population admixture. The method can handle any type of phenotype, including multiple phenotypes and missing parents, marker data, and/or phase, and provides both bi-allelic and multi-allelic tests. PowerFBAT is a tool for power simulation of association analysis using FBAT with binary outcomes. XWXW is an extension to the Haseman-Elston method for non-parametric linkage test with quantitative traits. XDT is a software that performs classical TDT, SDT and Rabinowitz TDT for nuclear families (not supported anymore). (entry from Genetic Analysis Software)

Proper citation: FBAT (RRID:SCR_009178) Copy   

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http://cran.r-project.org/web/packages/meta/index.html

Software application for fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot. (entry from Genetic Analysis Software)

Proper citation: R/META (RRID:SCR_009175) Copy   

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http://gaow.github.io/genetic-analysis-software/e-1.html#ehp

Software application that provides variance estimates for haplotype frequency estimates, it allows several kinds of missing information in the genotype data, it also allows for combined genotype data of different pool sizes. This program can be used for testing haplotype-disease associations in case control studies by calculating the likelihood ratio test: 2 log(likelihood for cases) + 2 log(likelihood for controls) - 2 log(likelihood for case+controls). (entry from Genetic Analysis Software)

Proper citation: EHP (RRID:SCR_009170) Copy   

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http://wpicr.wpic.pitt.edu/WPICCompGen/ehap__v1.htm

Software application detecting association between haplotypes and phenotypes (entry from Genetic Analysis Software)

Proper citation: EHAP (RRID:SCR_009169) 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://www.sanger.ac.uk/resources/software/amelia/

Software application that employs allele matching to analyse the effects of rare variants within a specific locus. 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, AMELIA has been developed as an allele-matching approach that is robust to the presence of both directions of effect for variants within the locus analysed. (entry from Genetic Analysis Software)

Proper citation: AMELIA (RRID:SCR_009119) Copy   

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http://www.decode.com/software/

Software application that is a faster version of GENEHUNTER and Allegro 1.2 (several degrees of increase of speed, can handle bigger families, up to 50 bits) (entry from Genetic Analysis Software)

Proper citation: ALLEGRO (RRID:SCR_009116) Copy   

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http://www.imbs.uni-luebeck.de/pub/sibsim/index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that simulates either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scalable way. It is based on XML, completely written in C++ and published under the GNU General Public License.

Proper citation: SIBSIM (RRID:SCR_009113) Copy   

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

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

Proper citation: IGG (RRID:SCR_009114) 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)

Proper citation: QTLNETWORK (RRID:SCR_009078) Copy   

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http://pritch.bsd.uchicago.edu/treeld.html

Free software tool for mapping complex trait loci. TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data. (entry from Genetic Analysis Software)

Proper citation: TREELD (RRID:SCR_009111) 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://pritchardlab.stanford.edu/software.html

Software application that is a companion program to STRUCTURE that is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure. (entry from Genetic Analysis Software)

Proper citation: STRAT (RRID:SCR_009110) 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://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   

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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