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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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http://www.sph.umich.edu/csg/abecasis/Merlin

Software application that carries out single-point and multipoint analyses of pedigree data, including IBD and kinship calculations, nonparametric and variance component linkage analyses, error detection and information content mapping. For multipoint analyses in dense maps, Merlin allows the user to impose constraints on the number of recombinants between consecutive markers. Merlin estimates haplotypes by finding the most likely path of gene flow or by sampling paths of gene flow at all markers jointly. It can also list all possible nonrecombinant haplotypes within short regions. Finally, Merlin provides swap-file support for handling very large numbers of markers as well as gene-dropping simulations for estimating empirical significance levels. (entry from Genetic Analysis Software)

Proper citation: MERLIN (RRID:SCR_009289) 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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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://www.genetics.ucla.edu/software/

Software application for genetic analysis of human pedigree data under models involving a small number of loci. MENDEL is useful for segregation analysis, linkage calculations, genetic counseling, allele frequency estimation, and related kinds of problems. (entry from Genetic Analysis Software)

Proper citation: MENDEL (RRID:SCR_009288) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that uses as input a trio of files: 1) a LINKAGE-format locus file modified to contain locus name information; 2) a LINKAGE-format pedigree file; and 3) a map file. Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that then can automatically run these analyses (if you are using Mega2 in a Unix environment that supports C-shell scripts). (entry from Genetic Analysis Software)

Proper citation: MEGA2 (RRID:SCR_009286) Copy   

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http://www.mapqtl.nl

Software application for mapping of quantitative trait loci (QTLs) for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, full-sib family of outbreeders. Analyses: interval mapping, composite interval mapping, nonparametric mapping, automatic cofactor selection, permutation test for interval mapping. QTL charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software)

Proper citation: MAPQTL (RRID:SCR_009284) Copy   

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http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/

Software application (entry from Genetic Analysis Software)

Proper citation: MAPMAKER/EXP (RRID:SCR_009281) Copy   

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https://github.com/gaow/genetic-analysis-software/blob/master/pages/MAPMAKER%26HOMOZ.md

Software application that calculates multipoint lod scores in pedigrees with inbreeding loops (entry from Genetic Analysis Software)

Proper citation: MAPMAKER/HOMOZ (RRID:SCR_009282) 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://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.bioinf.mdc-berlin.de/~rohde/

Software program using loss of heterozygosity data to enhance the power to detect linkage in cancer families. (entry from Genetic Analysis Software)

Proper citation: LOH-LINKAGE (RRID:SCR_009259) Copy   

•   Source: SciCrunch Registry