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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Genotype-IBD Sharing Test Resource Report Resource Website 100+ mentions |
Genotype-IBD Sharing Test (RRID:SCR_006257) | GIST | software application, software resource, resource | Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix. | identical by descent, genotype, gene, genetic, genomic, unix, ms-windows, linux, linkage disequilibrium, linkage, association |
is listed by: Genetic Analysis Software has parent organization: Vanderbilt University; Tennessee; USA |
Vanderbilt Diabetes Center ; NHGRI HG00376; NIDDK DK62370; NHGRI N01-HG-15465 |
PMID:14872409 | nlx_154133 | http://phg.mc.vanderbilt.edu/content/gist | SCR_006257 | 2026-02-15 09:19:13 | 120 | ||||||
|
POOLSCORE Resource Report Resource Website |
POOLSCORE (RRID:SCR_007514) | software application, software resource | Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | SCR_009373, nlx_154595, nlx_154087 | SCR_007514 | R/POOLSCORE | 2026-02-15 09:19:37 | 0 | |||||||||
|
ENTROPY BLOCKER Resource Report Resource Website |
ENTROPY BLOCKER (RRID:SCR_000123) | ENTROPY BLOCKER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154300, nlx_154581, SCR_007247 | SCR_000123 | R/ENTROPY BLOCKER, R/ENTROPY_BLOCKER | 2026-02-15 09:17:52 | 0 | |||||||
|
Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, source code, software resource | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software https://bio.tools/ancestrymap |
http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-02-15 09:18:45 | 12 | ||||
|
R/TDTHAP Resource Report Resource Website 1+ mentions |
R/TDTHAP (RRID:SCR_007625) | software application, software resource | Software package for TDT with extended haplotypes in the R language. R is the public domain dialect of S. It should be possible to port this library to the commercial Splus product. The main problem would be translation of the help files. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/splus | is listed by: Genetic Analysis Software | nlx_154676, nlx_154602, SCR_000851 | http://www-gene.cimr.cam.ac.uk/clayton/software/ | SCR_007625 | TDTHAP | 2026-02-15 09:19:39 | 1 | ||||||||
|
R/FEST Resource Report Resource Website 1+ mentions |
R/FEST (RRID:SCR_013347) | software application, software resource | An R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154111, SCR_000830, nlx_154582 | SCR_013347 | FEST | 2026-02-15 09:20:45 | 2 | |||||||||
|
ENDOG Resource Report Resource Website 100+ mentions |
ENDOG (RRID:SCR_013289) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 77 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154299 | SCR_013289 | 2026-02-15 09:20:26 | 120 | |||||||||
|
MENDELSOFT Resource Report Resource Website |
MENDELSOFT (RRID:SCR_013177) | software application, software resource | Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux/cygwin, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154474 | SCR_013177 | 2026-02-15 09:20:39 | 0 | ||||||||||
|
BEAGLECALL Resource Report Resource Website 1+ mentions |
BEAGLECALL (RRID:SCR_013301) | BEAGLECALL | software application, software resource | Software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, ms-windows, unix, linux, macos | is listed by: Genetic Analysis Software | nlx_154239 | SCR_013301 | 2026-02-15 09:20:44 | 1 | |||||||||
|
SPREG Resource Report Resource Website 1+ mentions |
SPREG (RRID:SCR_013261) | SPREG | software application, software resource | Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | nlx_154660 | SCR_013261 | Secondary Phenotype REGression analysis | 2026-02-15 09:20:39 | 2 | ||||||||
|
HEGESMA Resource Report Resource Website 10+ mentions |
HEGESMA (RRID:SCR_013304) | software application, software resource | Software application for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154396 | SCR_013304 | HEterogeneity and GEnome Search Meta Analysis | 2026-02-15 09:20:42 | 14 | |||||||||
|
PYPOP Resource Report Resource Website 50+ mentions |
PYPOP (RRID:SCR_013425) | PYPOP | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, python, ms-windows, (98/2000/xp), linux | is listed by: Genetic Analysis Software | nlx_154559 | SCR_013425 | PYthon for POPulation genetics | 2026-02-15 09:20:28 | 70 | ||||||||
|
MDR Resource Report Resource Website 10+ mentions |
MDR (RRID:SCR_013427) | MDR | software application, software resource | Software application that is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions. (entry from Genetic Analysis Software) | gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
nlx_154096 | http://www.nitrc.org/projects/mdr | SCR_013427 | Multifactor Dimensionality Reduction | 2026-02-15 09:20:41 | 38 | |||||||
|
ANTMAP Resource Report Resource Website 10+ mentions |
ANTMAP (RRID:SCR_013426) | ANTMAP | software application, software resource | Software application based on the Ant Colony Optimization to solve the special case of the traveling salesman problem of ordering markers when the number of loci is large. ANYMAP performs segregation test, linkage grouping and locus ordering, and constructs a linkage map rapidly. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, ms-windows, macos, linux, unix, solaris | is listed by: Genetic Analysis Software | nlx_154226 | SCR_013426 | 2026-02-15 09:20:43 | 20 | |||||||||
|
GRIDQTL Resource Report Resource Website 10+ mentions |
GRIDQTL (RRID:SCR_013397) | GRIDQTL | software application, software resource | Publicly available Web-based application that can perform QTL mapping on a variety of population types. GridQTL will extend the functionality of QTLExpress by adding new and advanced approaches for modelling QTL analysis in simple and complex populations. These new methods will be available on a Grid system that will offer flexible workflow management, resource allocation, data persistence, detached execution of simulations and the scalability required for the increase in data volume, data sources and complexity required by the new models. (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based | is listed by: Genetic Analysis Software | Public | nlx_154215 | SCR_013397 | 2026-02-15 09:20:45 | 28 | ||||||||
|
TRIMHAP Resource Report Resource Website |
TRIMHAP (RRID:SCR_013512) | TRIMHAP | software application, software resource | Software application for linkage disequilibrium mapping based on ancestral founder haplotypes. Method uses haplotype data from general pedigrees. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, unix | is listed by: Genetic Analysis Software | nlx_154683 | SCR_013512 | TRIMmed-HAPlotype (previously named HAL: Haplotype ALgorithm) | 2026-02-15 09:20:47 | 0 | ||||||||
|
TOMCAT Resource Report Resource Website 10+ mentions |
TOMCAT (RRID:SCR_013120) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May24,2023. Software program that implements the Mantel statistics as proposed by Beckmann et al. (2005) to test for association between genetic markers and phenotypes in case-control studies using haplotype information. The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take into account linkage disequilibrium information between multiple markers, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for space time clustering, which we developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. Alternative measures for the phenotypic similarity were implemented. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, 5.0 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154681 | SCR_013120 | 2026-02-15 09:20:42 | 18 | |||||||||
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SASQUANT Resource Report Resource Website 1+ mentions |
SASQUANT (RRID:SCR_013122) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software) | gene, genetic, genomic, sas, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154610, biotools:sasquant | https://bio.tools/sasquant | SCR_013122 | 2026-02-15 09:20:40 | 4 | ||||||||
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SCORE-SEQ Resource Report Resource Website 1+ mentions |
SCORE-SEQ (RRID:SCR_013121) | software application, software resource | A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154611 | SCR_013121 | SCORE-type tests for detecting disease associations with rare variants in SEQuencing Studies | 2026-02-15 09:20:24 | 6 | |||||||||
|
QMSIM Resource Report Resource Website 50+ mentions |
QMSIM (RRID:SCR_013123) | software application, software resource | Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154560, biotools:qmsim | https://bio.tools/qmsim | SCR_013123 | Qtl and Marker SIMulator | 2026-02-15 09:20:38 | 57 |
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