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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TOMCAT Resource Report Resource Website 10+ mentions |
TOMCAT (RRID:SCR_013120) | software resource, software application | 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 | 2026-08-01 12:10:53 | 18 | |||||||||
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SCORE-SEQ Resource Report Resource Website 1+ mentions |
SCORE-SEQ (RRID:SCR_013121) | software resource, software application | 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 | 2026-08-01 12:11:01 | 6 | |||||||||
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SPERM Resource Report Resource Website 10+ mentions |
SPERM (RRID:SCR_009409) | software resource, software application | Software application for analysis of sperm typing data. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, fortran77 | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154656 | SCR_009409 | 2026-08-01 12:10:59 | 16 | |||||||||
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Solar Eclipse Imaging Genetics tools Resource Report Resource Website 10+ mentions |
Solar Eclipse Imaging Genetics tools (RRID:SCR_009645) | Solar Eclipse Imaging Genetics tools | software resource, software application | Software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Their focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data | c++, genetic association, genomic analysis, gifti, imaging genomics, linux, loni pipeline, macos, microsoft, nifti, posix/unix-like, snp, gene, windows, windows xp, genetics, neuroimaging, heritability, pleiotropy, quantitative trait loci, genome-wide association, gene expression, methylation, trait, structural neuroimaging, functionalneuroimaging, brain imaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Non-commercial, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552 | nlx_155966 | SCR_009645 | 2026-08-01 12:10:52 | 14 | ||||||||
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Movement Disorders Biobank Resource Report Resource Website |
Movement Disorders Biobank (RRID:SCR_010659) | MDBB | biomaterial supply resource, material resource | A biobank of human biological material and genetic information. It provides samples and information to researchers in order to identify new genes and clarify pathogenic mechanisms of diseases. The biobank offers biochemical and molecular diagnoses of genetic dystonias, Parkinson's disease and NBIA disorders, as well as storage of biological samples for external institutions. | dna, fibroblast, movement disorder, neurodegeneration, brain iron accumulation disorder, dystonia, parkinson's disease, phenotype, genotype, gene, biobank |
is listed by: One Mind Biospecimen Bank Listing is related to: EuroBioBank has parent organization: EuroBioBank |
Movement disorder, Neurodegeneration with Brain Iron Accumulation disorder, Dystonia, Parkinson's disease | nlx_69108 | http://www.istituto-besta.it/Area-Ricerca.aspx?doc=Elenco-Unita-Operative&IdUO=UO-NEUROGENETICAMOLECOLARE | SCR_010659 | 2026-08-01 12:10:52 | 0 | |||||||
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WHAIT Resource Report Resource Website |
WHAIT (RRID:SCR_009425) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software). | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154691 | SCR_009425 | Weighted Haplotype test And an Imputation-based Test. | 2026-08-01 12:10:59 | 0 | ||||||||
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ZAPLO Resource Report Resource Website 1+ mentions |
ZAPLO (RRID:SCR_009426) | ZAPLO | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. | gene, genetic, genomic, linux, unix, solaris | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154692 | SCR_009426 | 2026-08-01 12:11:01 | 3 | ||||||||
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UNKNOWN Resource Report Resource Website 10+ mentions |
UNKNOWN (RRID:SCR_009423) | UNKNOWN | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154684 | SCR_009423 | LINKAGE - general pedigrees | 2026-08-01 12:10:51 | 13 | ||||||||
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TFPGA Resource Report Resource Website 50+ mentions |
TFPGA (RRID:SCR_009421) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154680 | SCR_009421 | Tools For Population Genetic Analyses | 2026-08-01 12:11:01 | 57 | ||||||||
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ENDOG Resource Report Resource Website 100+ mentions |
ENDOG (RRID:SCR_013289) | software resource, software application | 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 | 2026-08-01 12:11:01 | 120 | |||||||||
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WEIGHTED FDR Resource Report Resource Website |
WEIGHTED FDR (RRID:SCR_013442) | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154604, SCR_000848, nlx_154690, biotools:weighted_fdr | https://bio.tools/weighted_fdr | SCR_013442 | R/WEIGHTED_FDR | 2026-08-01 12:11:02 | 0 | ||||||||
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GenGen Resource Report Resource Website 10+ mentions |
GenGen (RRID:SCR_013447) | GenGen | software resource, software application | A suite of free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated. | genomic analysis, imaging genomics, pathway, network, snp, gene, genetics, genomics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: OpenBioinformatics.org |
Free | nlx_155766 | http://www.nitrc.org/projects/gengen | SCR_013447 | GenGen: Genetic Genomics Analysis of Complex Data | 2026-08-01 12:11:04 | 25 | ||||||
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MENDELSOFT Resource Report Resource Website |
MENDELSOFT (RRID:SCR_013177) | software resource, software application | 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 | 2026-08-01 12:11:01 | 0 | ||||||||||
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BEAGLECALL Resource Report Resource Website 1+ mentions |
BEAGLECALL (RRID:SCR_013301) | BEAGLECALL | software resource, software application | 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 | 2026-08-01 12:10:54 | 1 | |||||||||
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SPREG Resource Report Resource Website 1+ mentions |
SPREG (RRID:SCR_013261) | SPREG | software resource, software application | 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 | 2026-08-01 12:11:03 | 2 | ||||||||
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HEGESMA Resource Report Resource Website 10+ mentions |
HEGESMA (RRID:SCR_013304) | software resource, software application | 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 | 2026-08-01 12:11:03 | 14 | |||||||||
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PyPop Resource Report Resource Website 50+ mentions |
PyPop (RRID:SCR_013425) | PyPop | software resource, software application | Open-source software pipeline for population genomics. Designed for processing genotype and allele data and running population genetic analyses, including conformity to Hardy-Weinberg expectations; tests for balancing or directional selection; estimates of haplotype frequencies and measures and tests of significance for linkage disequilibrium. | gene, genetic, genomic, python, ms-windows, (98/2000/xp), linux, macos | is listed by: Genetic Analysis Software | DOI:10.3389/fimmu.2024.1378512 | Free, Available for download, Freely available | nlx_154559 | https://github.com/alexlancaster/pypop, https://zenodo.org/records/19170148 | SCR_013425 | , Python for Population Genomics, PYthon for POPulation genetics | 2026-08-01 12:11:03 | 70 | |||||
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MDR Resource Report Resource Website 10+ mentions |
MDR (RRID:SCR_013427) | MDR | software resource, software application | 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 | 2026-08-01 12:10:54 | 38 | |||||||
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ANTMAP Resource Report Resource Website 10+ mentions |
ANTMAP (RRID:SCR_013426) | ANTMAP | software resource, software application | 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 | 2026-08-01 12:11:02 | 20 | |||||||||
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GRIDQTL Resource Report Resource Website 10+ mentions |
GRIDQTL (RRID:SCR_013397) | GRIDQTL | software resource, software application | 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 | 2026-08-01 12:11:03 | 28 |
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