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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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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IMPUTE Resource Report Resource Website 500+ mentions |
IMPUTE (RRID:SCR_009245) | IMPUTE | software resource, software application | Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software) | gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154411 | SCR_009245 | 2026-02-13 10:56:21 | 628 | |||||||||
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MDR-PDT Resource Report Resource Website 1+ mentions |
MDR-PDT (RRID:SCR_009243) | MDR-PDT | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154406 | SCR_009243 | Multifactor Dimensionality Reduction and genotype Pedigree Disequilibrium Test | 2026-02-13 10:56:21 | 2 | ||||||||
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INTERSNP Resource Report Resource Website 10+ mentions |
INTERSNP (RRID:SCR_009244) | INTERSNP | software resource, software application | Software application for genome-wide interaction analysis (GWIA) of case-control SNP data. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, unix, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154409 | SCR_009244 | genome-wide association and INTERaction analysis of SNP | 2026-02-13 10:56:21 | 18 | ||||||||
|
HTSNPER Resource Report Resource Website 1+ mentions |
HTSNPER (RRID:SCR_009242) | HTSNPER | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Java program for characterizing the haplotype block structure and selecting haplotype tagging SNP (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, jvm, ms-windows, linux | is listed by: Genetic Analysis Software | PMID:15740612 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154403 | SCR_009242 | Haplotype Tagging SNPer | 2026-02-13 10:56:21 | 2 | ||||||
|
HS-TDT Resource Report Resource Website 1+ mentions |
HS-TDT (RRID:SCR_009240) | HS-TDT | software resource, software application | Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154401, biotools:hs-tdt | https://bio.tools/hs-tdt | SCR_009240 | Haplotype Sharing Transmission Disequilibrium Test | 2026-02-13 10:56:21 | 4 | |||||||
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MARGARITA Resource Report Resource Website 1+ mentions |
MARGARITA (RRID:SCR_009279) | MARGARITA | software resource, software application | Software application that infers genealogies from population genotype data and uses these to map disease loci. These genealogies take the form of the Ancestral Recombination Graph (ARG). The ARG defines a genealogical tree for each locus, and as one moves along the chromosome the topologies of consecutive trees shift according to the impact of historical recombination events. (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | nlx_154460 | SCR_009279 | 2026-02-13 10:56:22 | 2 | |||||||||
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MAPINSPECT Resource Report Resource Website 100+ mentions |
MAPINSPECT (RRID:SCR_009277) | MAPINSPECT | software resource, software application | Software application that can be used to compare linkage maps obtained from different sources/populations/etc.. It will draw the linkage maps and look for common marker names, these are then connected in the drawing with dashed lines. All neighboring maps are compared in this way. Images can be printed and saved. Orders of the MAPs (ie which map is compared with which other map) can be changed and maps can be flipped (right mouse button). remark: MapComp bears close relationships with the GGT software package (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, delphi pascal, ms-window (32-bit) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154458 | SCR_009277 | GGT | 2026-02-13 10:56:22 | 324 | |||||||
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MAPDISTO Resource Report Resource Website 100+ mentions |
MAPDISTO (RRID:SCR_009275) | MAPDISTO | software resource, software application | Software program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. Its specificity is to propose recombination fraction estimates in case of segregation distortion. It can (1) compute and draw genetic maps easily and quickly through a graphical interface; (2) facilitate the analysis of marker data showing segregation distortion due to differential viability of gametes or zygotes. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, ms-excel | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154456 | SCR_009275 | 2026-02-13 10:56:22 | 115 | ||||||||
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MAP/MAP+/MAP+H/MAP2000 Resource Report Resource Website |
MAP/MAP+/MAP+H/MAP2000 (RRID:SCR_009272) | MAP/MAP+/MAP+H/MAP2000 | software resource, software application | Software application for multiple pairwise linkage analysis under interference (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, unix, sunos | is listed by: Genetic Analysis Software | nlx_154453 | SCR_009272 | (MAP+H is the radiation Hybrid module of MAP+) | 2026-02-13 10:56:22 | 0 | ||||||||
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MANTEL-STRUCT Resource Report Resource Website 1+ mentions |
MANTEL-STRUCT (RRID:SCR_009271) | MANTEL-STRUCT | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that tests for population structure through the use of Mantel tests (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154451 | SCR_009271 | 2026-02-13 10:56:22 | 4 | ||||||||
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MALDSOFT Resource Report Resource Website |
MALDSOFT (RRID:SCR_009269) | MALDSOFT | software resource, software application | Software program for admixture mapping of complex trait loci, using case-control data. The samples should come from a recently-admixed population; additional ''learning'' samples from the parental populations are helpful. (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, linux, ms-windows, (dos/window...) | is listed by: Genetic Analysis Software | nlx_154449 | SCR_009269 | 2026-02-13 10:56:22 | 0 | |||||||||
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SAGE Resource Report Resource Website 1000+ mentions |
SAGE (RRID:SCR_009302) | SAGE | software resource, software application | Software application that provides researchers with the tools necessary for various types of statistical genetic analysis of human family data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, version 4.0 will be in c++, unix, (dec unix/solaris), ms-windows, (95/nt), linux |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154606 | SCR_009302 | Statistical Analysis for Genetic Epidemiology | 2026-02-13 10:56:22 | 1029 | ||||||||
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PEDMANAGER Resource Report Resource Website |
PEDMANAGER (RRID:SCR_009300) | PEDMANAGER | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix | is listed by: Genetic Analysis Software | nlx_154491 | SCR_009300 | 2026-02-13 10:56:22 | 0 | |||||||||
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LRTAE Resource Report Resource Website 1+ mentions |
LRTAE (RRID:SCR_009265) | LRTAE | software resource, software application | Software application to compute a likelihood ratio test statistic that increases power to detect genetic association in the presence of phenotype, genotype, and/or haplotype misclassification errors. In addition, the program produces asymptotically unbiased estimates of frequency parameters. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, ms-windows, unix, solaris, linux | is listed by: Genetic Analysis Software | nlx_154443 | SCR_009265 | Likelihood Ratio Test Allowing for Errors | 2026-02-13 10:56:22 | 1 |
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