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

Software application to calculate pair-wise linkage disequilibrium based on SNP genotype data from unrelated individuals. EM algorithm is used to estimate pair-wise haplotype frequencies. The output file is in the format of input file for GOLD program, thus it can be directly plug into GOLD to get LD plots. (entry from Genetic Analysis Software)

Proper citation: EMLD (RRID:SCR_009171) Copy   

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http://www.ibms.sinica.edu.tw/~csjfann/first%20flow/programlist.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that for detecting linkage/disequilibrium signals # between genetic markers and disease loci, particularly if only one # or a few large pedigrees are available. The strategy differs from # conventional approaches that require at least a moderate number of # families to attain adequate statistical power. The proposed testing # procedure is advantageous in that it provides high statistical power # coupled with reduced sample collection. Furthermore, the proposed # method avoids problems such as potential population stratification # and genetic heterogeneity, and is robust with respect to misspecification # of phenotype. (entry from Genetic Analysis Software)

Proper citation: EPDT (RRID:SCR_009172) Copy   

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http://acgt.cs.tau.ac.il/gevalt/

Software application designed to simplify and expedite the process of genotype analysis and disease association tests by providing a common interface to several common tasks relating to such analyses. It is aimed for analysis of unrelated individuals as well as two-generation families. (entry from Genetic Analysis Software)

Proper citation: GEVALT (RRID:SCR_009207) Copy   

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

Software application that combines genetic map data and locus data to display Graphical Genotypes. Data can be viewed by individual or by linkage group, and sorted on markers. Statistics are calculated and simultaneous filtering/selection on multiple linkage groups is possible. Output of hi-res genotype drawings directly to printer or to emf/jpeg/bitmap image. A module for constructing GGT-datafiles from common mapmaker/joinmap style formatted data is available. (entry from Genetic Analysis Software)

Proper citation: GGT (RRID:SCR_009208) Copy   

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http://softlib.rice.edu/geno.html

Software application designed to identify genotypes that are likely to be errors. The statistical method was designed to identify typing error rather than pedigree errors, but is general enough to pinpoint any unlikely genotype still consistent with Mendelian inheritance. (entry from Genetic Analysis Software)

Proper citation: GENOCHECK (RRID:SCR_009203) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: EH (RRID:SCR_009168) Copy   

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http://www.geneweaveronline.com/

Software application for charting family medical/health history (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GENEWEAVER (RRID:SCR_009202) Copy   

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http://www.columbia.edu/~ws2267/SOFT/EAGLET/eaglet.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software package that provides a number of improved statistics for detecting linkage and estimating trait location. EAGLET uses multiple subsamples of dense SNP data to detect linkage with increased power, and to construct sharp 95% confidence intervals for the true trait location.

Proper citation: EAGLET (RRID:SCR_009166) Copy   

•   Source: SciCrunch Registry

http://nephrologie.uniklinikum-leipzig.de/nephrologie.site,postext,easylinkage.html

Software application that combines automated setup and performance of linkage analyses and simulation. The program package supports currently single-point linkage analyses, multi-point linkage analyses, and the simulation package SLink, and provides genome-wide as well as chromosomal postscript plots of LOD scores, NPL scores, P values, and other parameters. The software can analyze STRPs as well as SNP chip data from Affymetrix, Illumina, or self-defined SNP data. The program performs single- and multi-point simulation studies.

Proper citation: EASYLINKAGE/EASYLINKAGE-PLUS (RRID:SCR_009167) Copy   

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

Software application that implements a virtual computer world where biological entities are digital objects. In this world, each individual of a population is represented by a set of chromosomes with genetic elements (markers, genes, Quantitative Traits Loci, etc.) and attributes (phenotype, age, fertility, living status, exposure, etc.). It comes with a built-in model allowing basic genetic studies by simulations, performed according to parameter values such a penetrance matrix (phenotype probabilities for each genotype), exposure, between-relative mating probabilities, and a probability of migration in a two-dimensional migration process. The simulated populations could be analysed with different packages for statistical or genetical analysis (e.g., SAS, S-PLUS, Linkage, Mapmaker/sibs, Genehunter). Pedigrees can also be simulated according to a pedigree file at the LINKAGE format. (entry from Genetic Analysis Software)

Proper citation: GENOOM (RRID:SCR_009200) Copy   

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http://wwwcsif.cs.ucdavis.edu/~gusfield/dpph.html

Software application that is similar to the BPPH program (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DPPH (RRID:SCR_009164) Copy   

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

Software program that allows students and scientists to explore potential manifestations of genetic models and stochastic processes. It also provides a means to evaluate the effectiveness of statistical procedures such as linkage analysis or QTL detection. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GREGOR (RRID:SCR_009165) Copy   

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http://www.jurgott.org/linkage/LinkagePC.html

Software application - part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software)

Proper citation: MAKEPED (RRID:SCR_009162) 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 that manage genetic data (entry from Genetic Analysis Software)

Proper citation: DOLINK (RRID:SCR_009163) Copy   

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http://kumasakanatsuhiko.jp/projects/disentangler/

Software application that is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers. (entry from Genetic Analysis Software)

Proper citation: DISENTANGLER (RRID:SCR_009161) Copy   

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http://cougar.fhcrc.org/hplus/

An analysis tool for performing haplotype estimation on genetic markers such as SNPs and microsatellites. It is able to handle datasets that include case-control status as well as covariates and marker location variables (such as gene name, chromosome location, etc). (entry from Genetic Analysis Software)

Proper citation: HPLUS (RRID:SCR_009239) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: HIT (RRID:SCR_009236) Copy   

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

Software application that provides flexible simulations of family data within an easy-to-use, high-level programming language. GENETSIM has no limit on pedigree sizes or structures, or number of families, or number of marker, or number of chromosomes. Genetic transmission is modeled by first generating the locations of recombination events, and then performing gene dropping according to the given recombination pattern. Any pattern of missing data can be specified and genotyping errors can be simulated. GENETSIM can simulat multiple QTLs with pleiotropic effects, multivariate polygenic background and any number of environmental factors, age effects, epistasis and variable expression. Users can also select families based on ascertainment schemes by repeating simulations. (entry from Genetic Analysis Software)

Proper citation: GENETSIM (RRID:SCR_009199) Copy   

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http://vorlon.case.edu/~jxl175/HapMiner.html

Software application for association mapping based on directly mining the haplotypes from case-control data via a density-based clustering algorithm. HapMiner can be applied to whole-genome screens, as well as candidate-gene studies in small genomic regions. (entry from Genetic Analysis Software)

Proper citation: HAPMINER (RRID:SCR_009233) Copy   

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http://www.bioinf.mdc-berlin.de/projects/hap/

Haplotype estimation service available in two variants: one for genetic data from unrelated probands (e.g., case/control studies) and one for core family data (entry from Genetic Analysis Software)

Proper citation: HAPLOTYPE ESTIMATION (RRID:SCR_009231) Copy   

•   Source: SciCrunch Registry