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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-09 09:05:57 | 0 | ||||||||||
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Apache Hadoop Resource Report Resource Website 50+ mentions |
Apache Hadoop (RRID:SCR_011879) | Hadoop | software toolkit, software resource | Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets. | computing |
is listed by: OMICtools has parent organization: Apache Software Foundation |
Open unspecified license | OMICS_01210 | SCR_011879 | 2026-08-09 09:05:47 | 63 | ||||||||
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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 | 2026-08-09 09:06:15 | 1 | |||||||||
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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 | 2026-08-09 09:06:15 | 2 | ||||||||
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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 | 2026-08-09 09:05:57 | 17 | |||||||||
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PyPop Resource Report Resource Website 50+ mentions |
PyPop (RRID:SCR_013425) | PyPop | software application, software resource | 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 | 2026-08-09 09:06:17 | 74 | |||||
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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 | 2026-08-09 09:05:58 | 39 | |||||||
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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 | 2026-08-09 09:06:08 | 21 | |||||||||
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Statistics Calculator Resource Report Resource Website 10+ mentions |
Statistics Calculator (RRID:SCR_013827) | software application, software resource | A set of many statistics calculators, including a confidence interval calculator. | statistics, calculator, confidence interval calculator | Free, Available to the research community | SCR_013827 | 2026-08-09 09:06:14 | 12 | |||||||||||
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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 | 2026-08-09 09:06:17 | 28 | ||||||||
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Brain Decoder Toolbox Resource Report Resource Website 1+ mentions |
Brain Decoder Toolbox (RRID:SCR_013150) | BDTB | software application, software resource | Software that performs ?decoding? of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent. | analyze, japanese, linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ATR; Kyoto; Japan |
PMID:15852014 | GNU General Public Licence | nlx_155709 | http://www.nitrc.org/projects/bdtb | SCR_013150 | BrainDecoderToolbox | 2026-08-09 09:05:57 | 2 | |||||
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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) | 2026-08-09 09:06:18 | 0 | ||||||||
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PLABQTL Resource Report Resource Website 10+ mentions |
PLABQTL (RRID:SCR_012789) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154535 | SCR_012789 | PLAnt Breeding QTL analysis | 2026-08-09 09:05:55 | 14 | |||||||||
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HAPBLOCK 2 Resource Report Resource Website |
HAPBLOCK 2 (RRID:SCR_012788) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, stata | is listed by: Genetic Analysis Software | nlx_154376 | SCR_012788 | 2026-08-09 09:06:00 | 0 | ||||||||||
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ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software application, software resource | An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software) | genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: wANNOVAR has parent organization: OpenBioinformatics.org |
PMID:20601685 | Free | nlx_154225, biotools:annovar, OMICS_00165 | https://bio.tools/annovar, https://bio.tools/annovar | SCR_012821 | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-08-09 09:05:55 | 6463 | |||||
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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 | 2026-08-09 09:05:56 | 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 | 2026-08-09 09:06:04 | 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 | 2026-08-09 09:06:12 | 6 | |||||||||
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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 | 2026-08-09 09:05:56 | 63 | ||||||||
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INSEGT Resource Report Resource Website |
INSEGT (RRID:SCR_013126) | software application, software resource | Software application that constructs feasible haplotype configurations and the corresponding segregation types on pedigrees. the haplotype configuration minimizes recombinations on the pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, (the standard template library, stl, is used) | is listed by: Genetic Analysis Software | nlx_154412 | SCR_013126 | INference of SEGregation Types PANGAEA | 2026-08-09 09:05:56 | 0 |
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