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http://mather.well.ox.ac.uk/GLIDERS/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016.

Proper citation: GLIDERS (RRID:SCR_009210) Copy   

•   Source: SciCrunch Registry

http://ftp://statgen.ncsu.edu/pub/zaykin/

Software application performing a shuffling version of the exact conditional tests for different combinations of allelic and genotypic disequilibrium on haploid and diploid data, or their combination. (entry from Genetic Analysis Software)

Proper citation: MLD (RRID:SCR_009298) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.biomath.jussieu.fr/pub/mlbgh (not available)

Software application that is an extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method. (entry from Genetic Analysis Software)

Proper citation: MLBGH (RRID:SCR_009297) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/mitpene/mitpene.html (in Russian)

Software program for analysis of mitochondrial diseases (entry from Genetic Analysis Software)

Proper citation: MITPENE (RRID:SCR_009294) Copy   

•   Source: SciCrunch Registry

http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/index.html

Software application (entry from Genetic Analysis Software)

Proper citation: MKGST (RRID:SCR_009295) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Minimac

Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software)

Proper citation: MINIMAC (RRID:SCR_009292) Copy   

•   Source: SciCrunch Registry

http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software)

Proper citation: MFLINK (RRID:SCR_009290) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

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

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: HIT (RRID:SCR_009236) Copy   

•   Source: SciCrunch Registry