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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-02-13 10:56:22 | 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 | 2026-02-13 10:56:22 | 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 | 2026-02-13 10:56:22 | 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 | 2026-02-13 10:56:22 | 1 | |||||||
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HPLUS Resource Report Resource Website 10+ mentions |
HPLUS (RRID:SCR_009239) | HPLUS | software resource, software application | 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) | gene, genetic, genomic, ms-windows, linux | is listed by: Genetic Analysis Software | nlx_154400 | SCR_009239 | 2026-02-13 10:56:21 | 12 | |||||||||
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HIT Resource Report Resource Website |
HIT (RRID:SCR_009236) | HIT | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | nlx_154397 | SCR_009236 | Haplotype Inference Technique | 2026-02-13 10:56:21 | 0 | ||||||||
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GENETSIM Resource Report Resource Website |
GENETSIM (RRID:SCR_009199) | GENETSIM | software resource, software application | 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) | gene, genetic, genomic, octave, r (future version) | is listed by: Genetic Analysis Software | nlx_154341 | http://genetsim.org/ | SCR_009199 | 2026-02-13 10:56:20 | 0 | ||||||||
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HAPMINER Resource Report Resource Website |
HAPMINER (RRID:SCR_009233) | HAPMINER | software resource, software application | 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) | gene, genetic, genomic, ms-windows, linux | is listed by: Genetic Analysis Software | nlx_154390 | SCR_009233 | 2026-02-13 10:56:21 | 0 | |||||||||
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HAPLOTYPE ESTIMATION Resource Report Resource Website |
HAPLOTYPE ESTIMATION (RRID:SCR_009231) | HAPLOTYPE ESTIMATION | software resource, software application | 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) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154388 | SCR_009231 | 2026-02-13 10:56:21 | 0 | |||||||||
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HAPLOTTER Resource Report Resource Website 10+ mentions |
HAPLOTTER (RRID:SCR_009229) | HAPLOTTER | software resource, software application | 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) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | nlx_154386 | SCR_009229 | 2026-02-13 10:56:21 | 20 | |||||||||
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HAPLO.STAT Resource Report Resource Website 10+ mentions |
HAPLO.STAT (RRID:SCR_009227) | HAPLO.STAT | software resource, software application | A suite of routines for the analysis of indirectly measured haplotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic, s-plus 6.1.2, r 1.7.1, unix | is listed by: Genetic Analysis Software | nlx_154384 | SCR_009227 | previously HAPLO.SCORE | 2026-02-13 10:56:21 | 10 | ||||||||
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HAPLOPOOL Resource Report Resource Website |
HAPLOPOOL (RRID:SCR_009225) | HAPLOPOOL | software resource, software application | 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) | gene, genetic, genomic, gcc/g++, perl, matlab | is listed by: Genetic Analysis Software | nlx_154382 | SCR_009225 | 2026-02-13 10:56:21 | 0 | |||||||||
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HAPLORE Resource Report Resource Website 1+ mentions |
HAPLORE (RRID:SCR_009226) | HAPLORE | software resource, software application | Software application for haplotype reconstruction in general pedigree without recombination (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154383 | SCR_009226 | HAPLOtype REconstruction in pedigrees | 2026-02-13 10:56:21 | 5 | ||||||||
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LOH-LINKAGE Resource Report Resource Website |
LOH-LINKAGE (RRID:SCR_009259) | LOH-LINKAGE | software resource, software application | Software program using loss of heterozygosity data to enhance the power to detect linkage in cancer families. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154438 | SCR_009259 | 2026-02-13 10:56:21 | 0 | |||||||||
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LOCUSZOOM Resource Report Resource Website 500+ mentions |
LOCUSZOOM (RRID:SCR_009257) | LOCUSZOOM | software resource, software application | Software application designed to facilitate viewing of local association results together with useful information about a locus, such as the location and orientation of the genes it includes, linkage disequilibrium coefficients and local estimates of recombination rates. It was developed by popular demand, as a result of many questions we have had about How did you make the figures in your talk? or How did you make the figures for your GWAS paper? (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154436 | SCR_009257 | 2026-02-13 10:56:22 | 719 | |||||||||
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LAMARC Resource Report Resource Website 10+ mentions |
LAMARC (RRID:SCR_009252) | LAMARC | software resource, software application | Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, ms-windows, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1016/j.tree.2008.09.007 | OMICS_28408, nlx_154420 | https://sources.debian.org/src/lamarc/ | SCR_009252 | Likelihood Analysis with Metropolis Algorithm using Random Coalescence | 2026-02-13 10:56:21 | 46 | ||||||
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LINKAGE-IMPRINT Resource Report Resource Website |
LINKAGE-IMPRINT (RRID:SCR_009253) | LINKAGE-IMPRINT | software resource, software application | Software application that is a parametric model-based approach to analyzing pedigree data for genomic imprinting. They have modified widely used LINKAGE program to incorporate imprinting. In addition, the LINKAGE-IMPRINT program allows for the use of sex-specific recombination in the analysis, which is of particular importance in a genome-wide analysis for imprinted genes. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, pascal, unix, solaris | is listed by: Genetic Analysis Software | nlx_154430 | SCR_009253 | LINKAGE allowing for IMPRINITING | 2026-02-13 10:56:22 | 0 | ||||||||
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KING Resource Report Resource Website 1000+ mentions |
KING (RRID:SCR_009251) | KING | software resource, software application | Software toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) for applications such as family relationship inference and population structure identification (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, (64bit), ms-windows, ms-dos, macos, ubuntu, (32bit) | is listed by: Genetic Analysis Software | nlx_154419 | SCR_009251 | Kinship-based INference for Gwas | 2026-02-13 10:56:21 | 1124 | ||||||||
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JLIN Resource Report Resource Website 1+ mentions |
JLIN (RRID:SCR_009247) | JLIN | software resource, software application | Software application designed for customizable, intuitive visualisation of LD analysis across all common computing platforms. Customisation allows the researcher to choose particular visualisation, statistical measures and measurement ranges. JLIN also allows the researcher to export images of the LD visualisation in several common document formats. As there appears to be no single best measure of LD under all possible circumstances, JLIN allows the researcher to visually compare and contrast the results of a range of statistical measures on the input data set(s). These measures include the commonly used D'' and R2 statistics and empirical p-values. New additions include calculation of HWE, a completely revamped interface, and a numer of minor bug fixes. We have added a display measure to show marker distances visually, embedded fonts to improve image clarity and additional LD measures including d,OR,Pexcess and Q. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, any with java 1.5 support | is listed by: Genetic Analysis Software | nlx_154415 | SCR_009247 | Java based LINkage disequilibrium plotter | 2026-02-13 10:56:21 | 9 | ||||||||
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JOINMAP Resource Report Resource Website 1000+ mentions |
JOINMAP (RRID:SCR_009248) | JOINMAP | software resource, software application | Software application for construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family. Can combine (''join'') data derived from several sources into an integrated map. Further: linkage group determination, automatic phase determination for outbreeders full-sib family, several diagnostics, and map 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_154416 | SCR_009248 | Software for the calculation of genetic linkage maps | 2026-02-13 10:56:21 | 1049 |
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