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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019. | temporal, signal, clocklikeness, molecular, phylogeny, visualization, analysis, temporally, sampled, sequenced, data, identify, genetic, incongruent | is related to: BEAST | ERC Grant ; EU Seventh Framework Programme |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | Path-O-Gen, tempest | 2026-09-03 04:54:28 | 166 | ||||||
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European Variation Archive (EVA) Resource Report Resource Website 100+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | data or information resource, data repository, database, service resource, storage service resource | Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser. | Collection, genetic, variation, data, chromosomal, location, dbSNP, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:eva | https://bio.tools/eva | SCR_017425 | EVA, European Variation Archive | 2026-09-03 04:54:24 | 107 | ||||||
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Cardiff Study of all Wales and North West of England Twins Resource Report Resource Website |
Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) | CaStANET | data or information resource | Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people. | Twins, family, genetic, environmental, origin, trait, collected, behavioral, psychopathological, data | PMID:17539361 | SCR_017480 | 2026-09-03 04:54:29 | 0 | ||||||||||
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GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | analysis service resource, atlas, data analysis service, data or information resource, database, production service resource, service resource | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | Gene ATLAS, Gene Atlas | 2026-09-03 04:54:32 | 158 | |||||||||
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GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | data analysis software, data processing software, software application, software resource | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-09-03 04:54:44 | 3 | |||||
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Aevol Resource Report Resource Website 1+ mentions |
Aevol (RRID:SCR_015966) | simulation software, software application, software resource | Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences). | software, genetic, model, simulation, evolution, microorganism, coding, sequence, algorithm | Agence Nationale de la Recherche ANR-10-BLAN-1724; INSERM |
PMID:24278000 | Free, Available for download, Tutorial available | SCR_015966 | 2026-09-03 04:53:22 | 3 | |||||||||
|
Bio++ Resource Report Resource Website 50+ mentions |
Bio++ (RRID:SCR_016055) | software application, software development tool, software library, software resource, software toolkit | Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic, molecular evolution, genetic, program, write, tool, visualize, edit, print, data, bioinformatic, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15696, biotools:biopp | https://sources.debian.org/src/bppsuite/, https://groups.google.com/forum/#!categories/biopp-help-forum/all-questions, https://github.com/BioPP, https://bio.tools/biopp, | SCR_016055 | Bppsuite, Bppphyview, Bio++ program suite, Bio++ Phylogenetic Viewer | 2026-09-03 04:53:45 | 65 | |||||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NIGMS R01 ; NIH R01 AI47745; NIH U01 AI43638; NSF DBI-0096033; NSF DEB-9996118; University of California Universitywide AIDS Research Program IS02-SD-701; University of California ; San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214 |
PMID:15509596 | Free, Available for download, Freely available | SCR_016271, biotools:HyPhy, OMICS_04235 | https://sources.debian.org/src/hyphy-pt/, https://veg.github.io/hyphy-site/, https://github.com/veg/hyphy, https://bio.tools/HyPhy, | SCR_016162 | HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt | 2026-09-03 04:53:36 | 1586 | |||||
|
Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. | editing, database, management, plasmid maps, restriction, ligation, alignments, sequence, data, import, calculator, gel, image, display, PCR, cloning, genetic |
is listed by: Debian is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Free Software Foundation | Free, Available for download | OMICS_18307 | https://sources.debian.org/src/gentle/ | SCR_016127 | GENtle | 2026-09-03 04:53:48 | 6 | ||||||
|
NIMH Repository and Genomics Resources (NRGR) Resource Report Resource Website 10+ mentions |
NIMH Repository and Genomics Resources (NRGR) (RRID:SCR_016318) | NRGR, RGR | institution | Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness. | biosamples, genetic, pedigree, clinical, data |
is recommended by: National Library of Medicine works with: NCBI database of Genotypes and Phenotypes (dbGap) works with: Gene Expression Omnibus (GEO) works with: NIMH Data Archive |
NIMH | Restricted | grid.482687.7 | https://ror.org/026dax180 | SCR_016318 | NRGR, Repository and Genomics Resources, NIMH, RGR | 2026-09-03 04:53:34 | 29 | |||||
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Tests for deviation from Hardy-Weinberg equilibrium Resource Report Resource Website 10+ mentions |
Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) | data analysis software, data processing software, software application, software resource | Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases. | deviation, Hardy-Weinberg, equilibrium, test, association, population, genetic, identify, susceptibility, gene, disease, single, nucleotide, polymorphisms, snp, allele | SCR_016496 | 2026-09-03 04:53:50 | 18 | ||||||||||||
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Cardiovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) | data or information resource, database, disease-related portal, portal, topical portal | Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data. | genetic, data, cardiovascular, disease, human | is listed by: NIDDK Information Network (dkNET) | cardiovascular disease, myocardial infarction, atrial fibrillation | Accelerating Medicines Partnership in Type 2 Diabetes ; National Institute of Cardiovascular Diseases and Stroke |
Free, Available for download, Google ID required, Tutorial available | SCR_016536 | 2026-09-03 04:53:41 | 31 | ||||||||
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Cerebrovascular Disease Knowledge Portal Resource Report Resource Website 1+ mentions |
Cerebrovascular Disease Knowledge Portal (RRID:SCR_016535) | portal, disease-related portal, topical portal, data or information resource | Platform for searching and analysis of human genetic information linked to cerebrovascular disease while protecting the integrity and confidentiality of the data. | human, genetic, information, cerebrovascular, disease, data, knowledge |
has parent organization: Broad Institute of MIT and Harvard has parent organization: Massachusetts General Hospital |
cerebrovascular disease | Accelerating Medicines Partnership in Type 2 Diabetes ; National Institute of Neurological Disorders and Stroke |
Free, Available for download, Google ID required, Tutorial available | SCR_016535 | 2026-09-03 04:54:04 | 9 | ||||||||
|
Cerebrovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) | CDKP | data or information resource, database, disease-related portal, portal, topical portal | Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data. | human, genetic, information, cerebrovascular, disease, data, knowledge |
is listed by: NIDDK Information Network (dkNET) has parent organization: Massachusetts General Hospital Labs and Facilities |
cerebrovascular disease | Accelerating Medicines Partnership in Type 2 Diabetes ; NIH ; NINDS |
Free, Available for download | SCR_016535 | SCR_015628 | Cerebrovascular Disease Knowledge Portal (CDKP) | 2026-09-03 04:53:15 | 17 | |||||
|
Ontology for Genetic Interval Resource Report Resource Website |
Ontology for Genetic Interval (RRID:SCR_003423) | OGI | controlled vocabulary, data or information resource, ontology | An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure. | owl, genomic, genetic, dna, rna, allele, marker, chromosome, rna molecule |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157517 | https://bioportal.bioontology.org/ontologies/OGI | SCR_003423 | 2026-09-03 04:57:39 | 0 | |||||||
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SNPFILE Resource Report Resource Website 1+ mentions |
SNPFILE (RRID:SCR_009402) | software application, software library, software resource, software toolkit | Software library and API for manipulating large SNP datasets with associated meta-data, such as marker names, marker locations, individuals'' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPFile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, unix | is listed by: Genetic Analysis Software | nlx_154641 | SCR_009402 | 2026-09-03 04:58:08 | 1 | ||||||||||
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PLEXdb - Plant Expression Database Resource Report Resource Website 10+ mentions |
PLEXdb - Plant Expression Database (RRID:SCR_006963) | PLEXdb | analysis service resource, data analysis service, data or information resource, data repository, database, portal, production service resource, service resource, storage service resource, topical portal | PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets. | gene expression, plant, plant pathogen, genotype, phenotype, genetic, physical, pathway, plant biology, compare, functional genomics, expression profiling, expression atlas, pathogen, genome, anova, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: FuncExpression has parent organization: Iowa State University; Iowa; USA |
UniNSF DBI-0543441; NSF IOS-0922746; USDA 3625-21000-049-00D |
PMID:22084198 | biotools:plexdb, r3d100011516, nlx_149236 | https://bio.tools/plexdb, https://doi.org/10.17616/R39D13 | SCR_006963 | PLEXdb - Gene expression resources for plants and plant pathogens, Plant Expression Database | 2026-09-03 04:58:04 | 21 | |||||
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Genetic and Rare Diseases Information Center Resource Report Resource Website 10+ mentions |
Genetic and Rare Diseases Information Center (RRID:SCR_008695) | GARD | data or information resource, disease-related portal, portal, topical portal | Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. | genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical | has parent organization: National Institutes of Health | Office of Rare Diseases Research ; NHGRI |
nif-0000-37627 | SCR_008695 | Genetic Rare Diseases Information Center | 2026-09-03 04:58:13 | 16 | |||||||
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Pig Genome Mapping Resource Report Resource Website |
Pig Genome Mapping (RRID:SCR_012884) | PiGMaP | atlas, data or information resource, database, image collection | Map of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality. | gene, genetic, artificial chromosome, bacteriophage, biological, carcass, cattle, cdna, comparative, disease, genome, genotype, growth, human, karyotpe, linkage, livestock, locus, map, mapping, marker, mice, molecular, p1, pig, quality, quantitative, sus scrofa, trait, yeast | has parent organization: Roslin Institute | PMID:7749223 | nif-0000-20987 | http://www.projects.roslin.ac.uk/pigmap/pigmap.html | SCR_012884 | PGM | 2026-09-03 04:58:18 | 0 | ||||||
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UC Davis Genome Center Labs and Facilities Resource Report Resource Website 1+ mentions |
UC Davis Genome Center Labs and Facilities (RRID:SCR_012480) | UCD Genome Center Labs & Facilities, UCD Genome Center Labs and Facilities | access service resource, core facility, data or information resource, organization portal, portal, service resource, training service resource | Genome Center uses technologies to understand how heritable genetic information of diverse organisms functions in health and disease. Provides research facilities, service cores, and staff for genomics research and training. Core facilities for Bioinformatics,DNA Technologies and Expression Analysis, Metabolomics, Proteomics,TILLING Core,Yeast One Hybrid Services Core. | Heritable, genetic, information, diverse, organism, function, health, disease, core, facility, service, genomic, training, |
is listed by: ScienceExchange is related to: University of California at Davis Genome Center Proteomics Core Facility has parent organization: University of California at Davis; California; USA |
SciEx_227, SCR_012659, SciEx_756 | https://genomecenter.ucdavis.edu/ | http://www.scienceexchange.com/facilities/uc-davis-genome-center-uc-davis | SCR_012480 | University of California Davis Genome Center Labs and Facilities, UC Davis Genome Center Labs & Facilities, University of California Davis Genome Center Labs & Facilities | 2026-09-03 04:58:15 | 3 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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