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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CHIAMO Resource Report Resource Website 1+ mentions |
CHIAMO (RRID:SCR_009150) | CHIAMO | software resource, software application | Software application for calling genotypes from the Affymetrix 500K Mapping chip. The program allows for multiple cohorts which have potentially different intensity characteristics that can lead to elevated false-positive rates in genome-wide studies. The underlying model has a hierarchical structure that allows for correlation between the parameters of each cohort. The output files produced by CHIAMO feed directly into both the programs SNPTEST and IMPUTE. CHIAMO was used to call genotypes for the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154269 | http://www.stats.ox.ac.uk/~marchini/software/gwas/chiamo.html | SCR_009150 | 2026-02-14 02:07:14 | 2 | ||||||||
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CHECKMATRIX Resource Report Resource Website 1+ mentions |
CHECKMATRIX (RRID:SCR_009149) | CHECKMATRIX | software resource, software application | Software application that serves as a visualization tool to validate constructed genetic maps. CheckMatrix generates graphical genotypes and two-dimensional heat plots of pairwise scores. Visualization of regions with positive and negative linkage as well as of allele fraction per marker simplifies genetic map validation without applying statistical approaches. CheckMatrix works in conjunction with MadMapper and freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software) | gene, genetic, genomic, python | is listed by: Genetic Analysis Software | nlx_154268 | SCR_009149 | PY_MATRIX_D | 2026-02-14 02:06:59 | 9 | ||||||||
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CFC Resource Report Resource Website |
CFC (RRID:SCR_009146) | CFC | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. General-purpose program for monitoring genetic diversity. CFC allows for several pedigree analyses such as: (1) computing inbreeding coefficients and relationships; (2) computing average relationships very quickly within and between specified groups of individuals; (3) computing average relatedness; (4) ancestral decomposition of the average or the individual inbreeding coefficient; (5) ancestral decomposition of the average coancestry; (6) optimizing matings to minimize the average inbreeding coefficients in the next generation; (7) computing founder equivalent, founder genome equivalent and effective number of non-founders; (8) computing numerator relationship matrix, its Cholesky decomposition and its inverse; (9) providing useful information on the structure of pedigrees. | gene, genetic, genomic, visual c++, ms-windows, (98/nt/xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154264 | SCR_009146 | Inbreeding (F) and Coancestry, Contribution | 2026-02-14 02:07:14 | 0 | |||||||
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CEPH2MAP Resource Report Resource Website |
CEPH2MAP (RRID:SCR_009144) | CEPH2MAP | software resource, software application | Software application developed from crimap v2.4 for use with the map suite of programs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | nlx_154263 | SCR_009144 | 2026-02-14 02:07:08 | 0 | |||||||||
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EVOKER Resource Report Resource Website 1+ mentions |
EVOKER (RRID:SCR_009145) | EVOKER | software resource, software application | A graphical tool for visualizing genotype intensity data in order to assess genotype calls as part of quality control procedures for genome-wide association studies. It provides a solution to the computational and storage problems related to being able to work with the huge volumes of data generated by such projects by implementing a compact, binary format that allows rapid access to data, even with hundreds of thousands of observations. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, perl | is listed by: Genetic Analysis Software | nlx_154305 | SCR_009145 | 2026-02-14 02:06:59 | 8 | |||||||||
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CCREL Resource Report Resource Website |
CCREL (RRID:SCR_009142) | CCREL | software resource, software application | Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, perl, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:ccrel, nlx_154261 | https://bio.tools/ccrel | SCR_009142 | Case-Control association analysis with RELlated individuals | 2026-02-14 02:07:14 | 0 | |||||||
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HAPAR Resource Report Resource Website |
HAPAR (RRID:SCR_009218) | HAPAR | software resource, software application | Software application to infer haplotype from genotype data. It uses the parsimony principle, i.e. try to find the minimum number of haplotypes that can reconstruct the input genotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-window, unix, solaris | is listed by: Genetic Analysis Software | nlx_154373 | SCR_009218 | HAplotype inference by PARsimony | 2026-02-14 02:07:01 | 0 | ||||||||
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HAP 2 Resource Report Resource Website |
HAP 2 (RRID:SCR_009217) | HAP 2 | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, ms-windows, unix, solaris, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154372 | SCR_009217 | HAPlotype analysis of polymorphic markers | 2026-02-14 02:07:10 | 0 | |||||||
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GTOOL Resource Report Resource Website 10+ mentions |
GTOOL (RRID:SCR_009215) | GTOOL | software resource, software application | Software application for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154368 | SCR_009215 | 2026-02-14 02:07:15 | 42 | |||||||||
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GMCHECK Resource Report Resource Website |
GMCHECK (RRID:SCR_009213) | GMCHECK | software resource, software application | Software application that finds the posterior probabilities for data errors for genotypes and phenotypes in pedigree data (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | nlx_154362 | http://episun7.med.utah.edu/~alun/gmcheck/ | SCR_009213 | 2026-02-14 02:07:10 | 0 | ||||||||
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GLIDERS Resource Report Resource Website 1+ mentions |
GLIDERS (RRID:SCR_009210) | GLIDERS | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154359 | SCR_009210 | Genome-wide LInkage DisEquilibrium Repository and Search engine | 2026-02-14 02:07:15 | 1 | |||||||
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GEVALT Resource Report Resource Website 1+ mentions |
GEVALT (RRID:SCR_009207) | GEVALT | software resource, software application | 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) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154354 | SCR_009207 | GEnotype Visualization and ALgorithmic Tool | 2026-02-14 02:06:47 | 6 | ||||||||
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GGT Resource Report Resource Website 1+ mentions |
GGT (RRID:SCR_009208) | GGT | software resource, software application | 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) | gene, genetic, genomic, delphi, (pascal), ms-windows, (95/98/2000/xp) | is listed by: Genetic Analysis Software | nlx_154356 | http://www.dpw.wau.nl/pv/PUB/ggt/ | SCR_009208 | Graphical GenoTyping package MAPCOMP | 2026-02-14 02:07:09 | 1 | |||||||
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GENOCHECK Resource Report Resource Website 1+ mentions |
GENOCHECK (RRID:SCR_009203) | GENOCHECK | software resource, software application | 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) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154345 | SCR_009203 | GenoCheck | 2026-02-14 02:06:47 | 7 | ||||||||
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GENEWEAVER Resource Report Resource Website 10+ mentions |
GENEWEAVER (RRID:SCR_009202) | GENEWEAVER | software resource, software application | 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. | gene, genetic, genomic, ms-windows, (95/98/2000/nt/xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154343 | SCR_009202 | 2026-02-14 02:07:15 | 39 | ||||||||
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GENOOM Resource Report Resource Website |
GENOOM (RRID:SCR_009200) | GENOOM | software resource, software application | 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) | gene, genetic, genomic, c++, unix, linux | is listed by: Genetic Analysis Software | nlx_154350 | http://www.genoom.com/ | SCR_009200 | GENetic Object Oriented Modeling in population genetics | 2026-02-14 02:07:09 | 0 | |||||||
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MEGA2 Resource Report Resource Website 100+ mentions |
MEGA2 (RRID:SCR_009286) | MEGA2 | software resource, software application | 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) | gene, genetic, genomic, c, unix, (solaris, silicon graphics, osf1, macos x), linux, ms-windows, macos, (x) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154471 | SCR_009286 | a Manipulation Environment for Genetic Analyses | 2026-02-14 02:07:17 | 114 | |||||||
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MAPQTL Resource Report Resource Website 100+ mentions |
MAPQTL (RRID:SCR_009284) | MAPQTL | software resource, software application | 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) | gene, genetic, genomic, ansi c, delphi, ms-windows, (95/98/me/nt4.0/2000) | is listed by: Genetic Analysis Software | nlx_154468 | SCR_009284 | Software for the calculation of QTL positions on genetic maps | 2026-02-14 02:07:11 | 392 | ||||||||
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MAPMAKER/EXP Resource Report Resource Website 100+ mentions |
MAPMAKER/EXP (RRID:SCR_009281) | MAPMAKER/EXP | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, vms, ms-dos, macos | is listed by: Genetic Analysis Software | nlx_154462 | SCR_009281 | MMDRAWER | 2026-02-14 02:07:04 | 282 | ||||||||
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MAPMAKER/HOMOZ Resource Report Resource Website 1+ mentions |
MAPMAKER/HOMOZ (RRID:SCR_009282) | MAPMAKER/HOMOZ | software resource, software application | Software application that calculates multipoint lod scores in pedigrees with inbreeding loops (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154463 | ftp://ftp-genome.wi.mit.edu/distribution/software/homoz | SCR_009282 | homozygosity mapping | 2026-02-14 02:07:17 | 1 |
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