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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   

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http://galton.uchicago.edu/genehunterplus

Software application that is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively). These files can then be used as input to the ASM program which incorporates the allele sharing modeling for lodscores and likelihood ratio tests as developed by Kong and Cox (1997). (entry from Genetic Analysis Software)

Proper citation: GENEHUNTER-PLUS (RRID:SCR_009193) Copy   

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http://www.biostat.jhsph.edu/~wmchen/gf.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software application that uses GEE method to estimate the location of the susceptibility gene based on the allele-sharing of affected sib pairs for multiple markers. GENEFINDER can further the analysis of GENEHUNTER by providing a more accurate gene location estimation and the corresponding confidence interval.

Proper citation: GENEFINDER (RRID:SCR_009190) Copy   

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http://hg-wen.uchicago.edu/selection/haplotter.htm

A web application that has been developed to display the results of a scan for positive selection in the human genome using the HapMap data. It can be used as a resource to examine various population genetic measures in a genomic region. Measures that are currently displayed include iHS (a statistic developed to detect recent positive selection), Fay and Wu''s H, Tajima''s D and Fst. (entry from Genetic Analysis Software)

Proper citation: HAPLOTTER (RRID:SCR_009229) Copy   

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http://mayoresearch.mayo.edu/mayo/research/biostat/schaid.cfm

A suite of routines for the analysis of indirectly measured haplotypes. (entry from Genetic Analysis Software)

Proper citation: HAPLO.STAT (RRID:SCR_009227) Copy   

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http://haplopool.icsi.berkeley.edu/haplopool/

Software program for estimating haplotype frequencies either from genotypes of individuals or from genotypes of pooled individuals. The genotypes must be for a block of bi-allelic SNPs (meaning that the SNPs should be in linkage disequilibrium with each other). The program assumes that it is given many genotypes of unrelated diploid individuals in Hardy-Weinberg equilibrium. If the genotypes are from pooled DNA, the program assumes that every pool contains the same number of individuals and the individuals were chosen at random when placed into the pools. For a reasonable running-time, the number of individuals in a pool needs to be between 2 and 4. (entry from Genetic Analysis Software)

Proper citation: HAPLOPOOL (RRID:SCR_009225) Copy   

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http://bioinformatics.med.yale.edu/group/software.html

Software application for haplotype reconstruction in general pedigree without recombination (entry from Genetic Analysis Software)

Proper citation: HAPLORE (RRID:SCR_009226) Copy   

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http://www.angelfire.com/mn2/nath/gems.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for fitting Genetic Epidemiology Models by running stochastic simulation in relation to disease dynamics.

Proper citation: GEMS (RRID:SCR_009188) Copy   

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http://www.mybiosoftware.com/genecounting-2-2-gene-counting-haplotype-analysis.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data.

Proper citation: GENECOUNTING (RRID:SCR_009189) Copy   

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http://episun7.med.utah.edu/~alun/gchap/index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals. By excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.

Proper citation: GCHAP (RRID:SCR_009186) Copy   

•   Source: SciCrunch Registry