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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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COVIBD Resource Report Resource Website |
COVIBD (RRID:SCR_009155) | software application, software resource | Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154207, SCR_009109, nlx_154275 | SCR_009155 | R/COVIBD | 2026-09-12 01:02:02 | 0 | |||||||||
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NIF Data Federation Resource Report Resource Website 10+ mentions |
NIF Data Federation (RRID:SCR_004834) | Data Federation | data or information resource, portal, service resource | Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below. | semantics, neuroscience, animal, annotation, antibody, biospecimen, brain activation foci, clinical trial, connectivity, dataset, disease, drug, grant, image, microarray, model, multimedia, negative data, pathway, people, plasmid, registry, software, brain region, cell, gene, molecule, multi-level, nervous system, nervous system function, model |
uses: MNI Podcasts uses: Educational Resources in Neuroscience uses: Mind Hacks uses: BAMS Nested Regions uses: Indeed uses: NINDS Disorder Index uses: Drug Design Data Resource uses: PubMed Health uses: This Week In Science uses: Science Talk uses: BAMS Connectivity uses: Lady Scientist uses: Psychology Corner uses: Wired Science uses: CENtral Science uses: RetractionWatch.com uses: The Guardian: Science Weekly uses: H2SO4Hurts uses: 60-Second Mind uses: PLoS Blogs uses: Clarity resources uses: Open Source Brain uses: Diabetic Complications Consortium uses: Integrated Animals uses: Kawasaki Disease Dataset uses: EEGbase uses: Integrated Models uses: Lifespan Observations Database uses: NIF Web Services uses: NIF Blog uses: ATCC uses: Cerebellar Platform uses: Brain Machine Interface Platform uses: Rafael Yustes Laboratory uses: ASAP uses: NIH VideoCasting uses: NIDA Data Share uses: Neurofed uses: Candida Genome Database uses: Addgene uses: ASPGD uses: Glomerular Activity Response Archive uses: WikiPathways uses: AmiGO uses: NeuroMorpho.Org uses: Cell Centered Database uses: Integrated uses: Community Structure-Activity Resource uses: ClinicalTrials.gov uses: Ensembl uses: GeneNetwork uses: Avian Brain Circuitry Database uses: EcoCyc uses: Entrez Gene uses: Zebrafish Information Network (ZFIN) uses: Arredondo ANT fNIRS dataset1 uses: Grants.gov uses: T3DB uses: Simtk.org uses: PharmGKB uses: DrugBank uses: Aging Genes and Interventions Database uses: Gene Expression Nervous System Atlas uses: SumsDB uses: bioDBcore uses: BioNumbers uses: Gene Ontology uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat uses: Gramene uses: Retina Project uses: HomoloGene uses: ArrayExpress uses: Journal of Visualized Experiments uses: Allen Mouse Brain Reference Atlas uses: Gene Weaver uses: Visiome Platform uses: Developmental Therapeutics Program uses: NeuroMab uses: WormBase uses: NeuronDB uses: Integrated Grants uses: studyforrest.org uses: BrainInfo uses: Mouse Phenome Database (MPD) uses: NCBI Taxonomy uses: NCBI Protein Database uses: Psychoactive Drug Screening Program Ki Database uses: Nuclear Receptor Signaling Atlas uses: Brede Database uses: NeuroImaging Tools and Resources Collaboratory (NITRC) uses: Mouse Genome Informatics Transgenes uses: Reactome uses: Cell Image Library (CIL) uses: BAMS Cells uses: Synapse Web uses: Integrated Videos uses: NeuroVault uses: Royal College of Psychiatrists Podcasts uses: WU-Minn HCP 500 Subjects MR and MEG Release uses: Data.gov Science and Research Data Catalog uses: NITRC-IR uses: One Mind Biospecimen Bank Listing uses: Integrated Brain Gene Expression uses: BrainSpan uses: All In The Mind uses: Scientific American Cross-Check uses: PubChem uses: NeuroPod uses: BrainSpan uses: Health.Data.gov uses: Biointeractive uses: UniProtKB uses: Gray Matters uses: dkCOIN uses: Brain Science Podcast uses: NIGMS Human Genetic Cell Repository uses: DISCO uses: GeneDB Lmajor uses: TAIR uses: ScienceNOW uses: Daily Scan uses: SGD uses: Integrated Software uses: BrainPod uses: GeneDB Tbrucei uses: MPO uses: PANTHER uses: Neurology Podcast uses: Integrated Disease uses: VMD uses: UCSF Laboratory for Visual Neuroscience uses: NIMH Chemical Synthesis and Drug Supply Program uses: NIH Neuroscience Microarray Consortium uses: SGN uses: Protocol Online - Your labs reference book uses: Integrated Podcasts uses: OpenNeuro uses: National Academy of Sciences Podcasts uses: Beta Cell Biology Consortium uses: Naturejobs uses: Scientific American Guest Blog uses: jobs.ac.uk uses: New Scientist Jobs uses: Science Careers uses: Access-ScienceJobs.co.uk uses: ScienceBlogs: Life Science uses: ScienceBlogs: Brain and Behavior uses: TheScienceJobs.com uses: Nature Network Blogs uses: The Guardian: Science uses: LabSpaces uses: ScienceBlogs: Medicine and Health uses: Scientific American Observations uses: Scientific American Bering in Mind uses: QUEST uses: Daring Nucleic Adventures - genegeek uses: Oxford Science Blog uses: Sciblogs uses: New York Times - Well uses: SciLogs uses: Cassandras Tears uses: BioPortfolio uses: Now at NEJM uses: 1000 Functional Connectomes Project uses: Integrated Jobs uses: Integrated Blogs uses: JCVI CMR uses: SciCrunch Registry uses: Neuroskeptic uses: CRCNS uses: Expression Atlas of the Marmoset uses: IXI dataset uses: Integrated Auto-Extracted Annotation uses: EU Clinical Trials Register uses: Integrated Clinical Trials uses: Human Brain Atlas uses: goCognitive uses: Law and Neuroscience uses: International Mouse Phenotyping Consortium (IMPC) uses: ClinVar uses: Integrated Gene-Disease Interaction uses: XNAT Central uses: neuroelectro uses: Integrated Nervous System Connectivity uses: Antibody Registry uses: OMIA - Online Mendelian Inheritance in Animals uses: OMIM uses: Science Podcast uses: Mouse Genome Informatics (MGI) uses: Monster uses: NCBI uses: Wired Science Blogs uses: F1000 Posters uses: Neurophilosophy uses: Comparative Toxicogenomics Database (CTD) uses: FlyBase uses: GeneReviews uses: GeneDB Pfalciparum uses: Naturally Selected uses: PomBase uses: Pseudomonas Genome Database uses: The Guardian: Science Videos uses: Orphanet uses: Dictyostelium discoideum genome database uses: PeptideAtlas uses: NeuroSynth uses: neuropathology blog uses: Genomes Unzipped uses: National Institutes of Health Research Portfolio Online Reporting Tool uses: BrainMaps.org uses: It Takes 30 uses: Gait in Parkinson's Disease uses: Physiobank uses: Gait Dynamics in Neuro-Degenerative Disease Data Base uses: American Journal of Psychiatry Podcasts uses: Neurodatabase.org uses: Brain Architecture Management System uses: RanchoBiosciences uses: ModelDB uses: CoCoMac uses: Olfactory Bulb Odor Map DataBase (OdorMapDB) uses: Gene Expression Omnibus uses: Caenorhabditis Genetics Center uses: Labome uses: Open Access Series of Imaging Studies uses: Biological General Repository for Interaction Datasets (BioGRID) uses: Olfactory Receptor DataBase uses: T1DBase uses: Gemma uses: CellML Model Repository uses: ResearchCrossroads uses: Biocompare uses: BioNOT uses: Hays uses: Research Blogging uses: Discover Magazine uses: PolygenicBlog uses: Kawasaki Disease Dataset2 uses: Allen Mouse Brain Connectivity Atlas uses: Integrated Manually Extracted Annotation uses: Roadmap Epigenomics Project uses: Integrated Cell Lines uses: National Mouse Metabolic Phenotyping Centers uses: Mendelspod uses: Integrated Snippets uses: Integrated Datasets uses: Nature Podcast uses: GWAS: Catalog of Published Genome-Wide Association Studies uses: KEGG uses: USC Multimodal Connectivity Database uses: Inside NIA: A Blog for Researchers uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: NIF Registry Automated Crawl Data uses: Genetic Analysis Software uses: anage uses: Intestinal Stem Cell Consortium uses: Animal QTLdb uses: elements of morphology uses: Human Life-Table Database uses: Clinical Genomic Database uses: NIDDK Central Repository uses: MONARCH Initiative uses: Human Phenotype Ontology is used by: SciCrunch is used by: NIDDK Information Network (dkNET) lists: AutDB lists: Drug Related Gene Database lists: Gene Ontology Tools lists: CHEBI is listed by: 3DVC is related to: International Mouse Strain Resource is related to: Internet Brain Volume Database is related to: Resource Identification Portal is related to: Rat Genome Database (RGD) is related to: VISTA Enhancer Browser is related to: NIH Human Pluripotent Stem Cell Registry is related to: Zebrafish International Resource Center is related to: Bloomington Drosophila Stock Center is related to: Journal of Comparative Neurology Antibody database has parent organization: Neuroscience Information Framework |
NIDA ; NIH Blueprint for Neuroscience Research ; U.S. Department of Health and Human Services HHSN27120080035C |
Refer to individual databases | nlx_81822 | http://neuinfo.org/nif/nifgwt.html?query=* | SCR_004834 | Neuroscience Information Framework Data Federation | 2026-09-12 01:00:55 | 28 | |||||
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LAPSTRUCT Resource Report Resource Website 1+ mentions |
LAPSTRUCT (RRID:SCR_007550) | software application, software resource | Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | Free | nlx_154589, SCR_009367, nlx_154209 | SCR_007550 | R/LAPSTRUCT, LAPlacian eigenfunctions learn population STRUCTure | 2026-09-12 01:00:57 | 3 | ||||||||
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Pedigree-Draw Resource Report Resource Website 1+ mentions |
Pedigree-Draw (RRID:SCR_008302) | commercial organization, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software) | gene, genetic, genomic, macos, bio.tools |
is listed by: Genetic Analysis Software is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154520, OMICS_00213, SCR_010795 | SCR_008302 | PEDIGREE/DRAW | 2026-09-12 01:00:58 | 1 | ||||||||
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EM-DECODER Resource Report Resource Website 1+ mentions |
EM-DECODER (RRID:SCR_000023) | EM-DECODER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program. | gene, genetic, genomic |
is listed by: Genetic Analysis Software has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154297 | SCR_000023 | 2026-09-12 01:02:22 | 1 | ||||||||
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HAPSCOPE Resource Report Resource Website |
HAPSCOPE (RRID:SCR_000838) | HAPSCOPE | software application, software resource | Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | PMID:12466546 | nlx_154393 | SCR_000838 | 2026-09-12 01:02:24 | 0 | ||||||||
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GENEHUNTER SAD Resource Report Resource Website |
GENEHUNTER SAD (RRID:SCR_000831) | GENEHUNTER SAD | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software application with implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154198 | SCR_000831 | 2026-09-12 01:02:24 | 0 | ||||||||
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COMDS Resource Report Resource Website |
COMDS (RRID:SCR_000832) | COMDS | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Software application for combined segregation and linkage analysis, incorporating severity and diathesis. (entry from Genetic Analysis Software) | gene, genetic, genomic, sun fortran, (the command fsplit is needed), unix, sunos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154255 | SCR_000832 | 2026-09-12 01:02:24 | 0 | ||||||||
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CHAPLIN Resource Report Resource Website 1+ mentions |
CHAPLIN (RRID:SCR_000833) | CHAPLIN | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Software application for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran90, (cvf 6.6) with imsl routines, ms-windows, (2000/xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154266 | SCR_000833 | Case-control HAPLotype INference package | 2026-09-12 01:02:24 | 2 | |||||||
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CRIMAP Resource Report Resource Website 1+ mentions |
CRIMAP (RRID:SCR_000834) | CRIMAP | software application, software resource | Software application for constructing multilocus linkage map (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, ms-windows, xp | is listed by: Genetic Analysis Software | PMID:7750973 | Source code available | nlx_154276 | http://compgen.rutgers.edu/Crimap/ | SCR_000834 | 2026-09-12 01:02:24 | 5 | ||||||
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ADEGENET Resource Report Resource Website 10+ mentions Issue |
ADEGENET (RRID:SCR_000825) | ADEGENET | software application, software resource | Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, r |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:21926124 PMID:18397895 DOI:10.1093/bioinformatics/btn129 |
Free, Available for download, Freely available | nlx_153996, nlx_154580, OMICS_11078, SCR_007239 | http://adegenet.r-forge.r-project.org/, https://sources.debian.org/src/r-cran-adegenet/ | SCR_000825 | R/ADEGENET | 2026-09-12 01:02:24 | 22 | |||||
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PEDIGREE-VISUALIZER Resource Report Resource Website |
PEDIGREE-VISUALIZER (RRID:SCR_000842) | PEDIGREE-VISUALIZER | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154521 | SCR_000842 | 2026-09-12 01:02:24 | 0 | |||||||||
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PEDPHASE Resource Report Resource Website |
PEDPHASE (RRID:SCR_000843) | PEDPHASE | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154525 | SCR_000843 | 2026-09-12 01:02:24 | 0 | ||||||||
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LOCUSMAP Resource Report Resource Website |
LOCUSMAP (RRID:SCR_000840) | LOCUSMAP | software application, software resource | Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 90/95, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154434, biotools:locusmap | https://bio.tools/locusmap | SCR_000840 | 2026-09-12 01:02:24 | 0 | ||||||||
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RHMAPPER Resource Report Resource Website |
RHMAPPER (RRID:SCR_000845) | RHMAPPER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154576 | SCR_000845 | 2026-09-12 01:02:24 | 0 | ||||||||
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GERMLINE Resource Report Resource Website 100+ mentions |
GERMLINE (RRID:SCR_001720) | GERMLINE | software application, software resource | Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c++, linux, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:18971310 | Free, Available for download, Freely available | biotools:germline, OMICS_00202, nlx_154080 | https://bio.tools/germline | http://www1.cs.columbia.edu/~gusev/germline/ | SCR_001720 | 2026-09-12 01:02:26 | 451 | |||||
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OLORIN Resource Report Resource Website |
OLORIN (RRID:SCR_002015) | OLORIN | software application, software resource | An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, any platform with java 1.6 or later, next generation sequencing, variant, haplotype, allele frequency, java swing |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: SourceForge |
PMID:23052039 | Free, Available for download, Freely available | nlx_154503, OMICS_01556 | http://sourceforge.net/p/olorin/ | SCR_002015 | 2026-09-12 01:02:27 | 0 | ||||||
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SIMIBD Resource Report Resource Website |
SIMIBD (RRID:SCR_002094) | SIMIBD | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, (sunos/solaris/hp/dec-unix) | is listed by: Genetic Analysis Software | PMID:9002040 | Free, Available for download, Freely available | nlx_154622 | http://watson.hgen.pitt.edu/register/soft_doc.html, http://watson.hgen.pitt.edu/~davis/ | SCR_002094 | 2026-09-12 01:02:27 | 0 | ||||||
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BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-09-12 01:02:26 | 390 | ||||||
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HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software application, software resource | A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, pedigree, haplotype, draw, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:15377505 | Free, Freely Available | nlx_154062, OMICS_00209, biotools:haplopainter | https://bio.tools/haplopainter | http://haplopainter.sourceforge.net/html/ManualIndex.htm | SCR_001710 | 2026-09-12 01:02:26 | 48 |
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