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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RTPrimerDB- The Real-Time PCR and Probe Database Resource Report Resource Website 10+ mentions |
RTPrimerDB- The Real-Time PCR and Probe Database (RRID:SCR_007106) | RTPrimerDB | data or information resource, data repository, database, storage service resource, service resource | Database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridization Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimization, and to introduce a certain level of uniformity and standardization among different laboratories. Researchers are encouraged to submit their validated primer and probe sequence, so that other users can benefit from their expertise. The database can be queried using the official gene name or symbol, Entrez or Ensembl Gene identifier, SNP identifier, or oligonucleotide sequence. Different options make it possible to restrict a query to a particular application (Gene Expression Quantification/Detection, DNA Copy Number Quantification/Detection, SNP Detection, Mutation Analysis, Fusion Gene Quantification/Detection, Chromatin immunoprecipitation (ChIP)), organism (Human, Mouse, Rat, and others) or detection chemistry. | primer, probe, sequence, real-time pcr, gene, assay, real-time pcr assay, FASEB list |
is listed by: OMICtools has parent organization: Ghent University; Ghent; Belgium |
PMID:18948285 PMID:16381959 PMID:12519963 |
Public, The community can contribute to this resource | nif-0000-03431, OMICS_02322 | SCR_007106 | 2026-08-05 10:44:36 | 48 | |||||||
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CD-HIT Resource Report Resource Website 1000+ mentions |
CD-HIT (RRID:SCR_007105) | CD-HIT | software resource, software application, data processing software, source code | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cluster, protein, sequence, classification, domain, analysis, nucleotide sequence, dna, protein sequence, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of California at San Diego; California; USA has parent organization: Google Code is parent organization of: CD-HIT-OTU |
NCRR 1R01RR025030 | PMID:20053844 PMID:16731699 DOI:10.1093/bioinformatics/btl158 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05157, biotools:cd-hit, nif-0000-30240 | http://cd-hit.org, https://code.google.com/p/cdhit/, https://bio.tools/cd-hit, https://sources.debian.org/src/cd-hit/ | http://bioinformatics.ljcrf.edu/cd-hi/ |
SCR_007105 | CD-HIT Program | 2026-08-05 10:44:36 | 3203 | |||
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BioRAT Resource Report Resource Website 1+ mentions |
BioRAT (RRID:SCR_007099) | BioRAT | text extraction software, software application, text-mining software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. An information extraction (IE) tool specifically designed to perform biomedical IE and which is able to locate and analyze both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE. | information extraction, search engine, biomedical, abstract, full-length paper |
is listed by: OMICtools is related to: Comparative Toxicogenomics Database (CTD) has parent organization: University College London; London; United Kingdom |
PMID:15231534 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_013452, nif-0000-21061, OMICS_01175 | SCR_007099 | Biological Research Assistant for Text mining | 2026-08-05 10:44:36 | 1 | ||||||
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Biological General Repository for Interaction Datasets (BioGRID) Resource Report Resource Website 1000+ mentions |
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) | BioGRID | data or information resource, database | Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. | budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics, bio.tools, FASEB list |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: OMICtools is listed by: DataCite is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: Pathway Commons is related to: Cytoscape is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: PSICQUIC Registry is related to: PSI-MI is related to: NIH Data Sharing Repositories is related to: Agile Protein Interactomes DataServer is related to: Integrated Manually Extracted Annotation has parent organization: Princeton University; New Jersey; USA has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: University of Montreal; Quebec; Canada works with: IMEx - The International Molecular Exchange Consortium |
NCRR R01 RR024031; NHGRI HG02223; Canadian Institutes of Health Research ; BBSRC ; NIH Office of the Director R24 OD011194 |
PMID:23203989 PMID:21071413 PMID:16381927 PMID:12620108 |
Free, Freely available | nif-0000-00432, r3d100010350, OMICS_01901, biotools:the_grid | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://bio.tools/the_grid, https://doi.org/10.17616/R34C7G | SCR_007393 | , BioGRID, Biological General Repository for Interaction Datasets | 2026-08-05 10:44:41 | 2554 | ||||
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YM500 Resource Report Resource Website |
YM500 (RRID:SCR_007429) | YM500 | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | An Integrative small RNA Sequencing database for miRNA research and provides an integrative web interface for miRNA quantification, isomiR identification, arm switching discovery, and, most of all, novel miRNA predictions. |
is listed by: OMICtools has parent organization: National Yang-Ming University; Taipei; Taiwan |
OMICS_00386 | SCR_007429 | YM500 miR-Seq Database | 2026-08-05 10:44:41 | 0 | |||||||||
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VISTA Enhancer Browser Resource Report Resource Website 100+ mentions |
VISTA Enhancer Browser (RRID:SCR_007973) | VISTA Enhancer Browser | data or information resource, data repository, database, storage service resource, service resource | Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. | human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NIF Data Federation is related to: One Mind Biospecimen Bank Listing is related to: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
American Heart Association ; NIDCR ; NHLBI HL066681; NHGRI HG003988; DOE contract DE-AC02-05CH11231; NINDS NS062859; DOE DE020060 |
PMID:17130149 | Free, Freely available | nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser | https://bio.tools/vista_enhancer_browser | SCR_007973 | 2026-08-05 10:44:52 | 233 | |||||
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ActiveDriver Resource Report Resource Website 10+ mentions |
ActiveDriver (RRID:SCR_008104) | ActiveDriver | data processing software, software application, sequence analysis software, data analysis software, software resource | A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications. | Protein sequence variation, variation interpretation, protein sequence, protein post-translational signaling modifications, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:ActiveDriver, OMICS_00140 | http://reimandlab.org/software/activedriver/, https://cran.r-project.org/web/packages/ActiveDriver/ActiveDriver.pdf, https://bio.tools/ActiveDriver | SCR_008104 | 2026-08-05 10:44:53 | 25 | |||||||
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QIIME Resource Report Resource Website 10000+ mentions |
QIIME (RRID:SCR_008249) | software resource, data processing software, software application, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics. | microbiome, microbial community, sequence data, data analysis software, bio.tools |
is used by: SortMeRNA is used by: Nephele is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
DOI:10.1038/nmeth.f.303 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01118, SCR_011948, OMICS_01521, biotools:qiime | https://bio.tools/qiime | SCR_008249 | Quantitative Insights Into Microbial Ecology | 2026-08-05 10:44:58 | 11036 | ||||||
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Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | data processing software, web application, software application, data analysis software, sequence analysis software, software resource | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-08-05 10:44:59 | 3542 | |||||
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Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | data processing software, software application, data visualization software, data analysis software, software toolkit, software resource | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/, https://github.com/avogadro, https://bio.tools/avogadro, https://sources.debian.org/src/axe-demultiplexer/ | SCR_015983 | 2026-08-05 10:46:31 | 1965 | ||||||
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Short Read Sequence Typing for Bacterial Pathogens Resource Report Resource Website 10+ mentions |
Short Read Sequence Typing for Bacterial Pathogens (RRID:SCR_015870) | SRST2 | data processing software, source code, software application, data analysis software, sequence analysis software, software resource | Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. | genotype analysis, illumina sequence data, mlst database, gene sequence, st, reference gene, short read |
uses: Bowtie uses: SAMTOOLS is listed by: Debian is listed by: OMICtools requires: SciPy requires: Python Programming Language |
infectious disease | NHMRC of Australia 1043830; NHMRC of Australia 1061409; NHMRC of Australia 1061435; Victorian Life Sciences Computation Initiative (VLSCI) VR0082 |
PMID:25422674 | Free, Available for download | OMICS_12777 | http://katholt.github.io/srst2/, https://sources.debian.org/src/srst2/ | http://srst.sourceforge.net/ | SCR_015870 | SRST2: Short Read Sequence Typing for Bacterial Pathogens, Short Read Sequence Typing v2 | 2026-08-05 10:46:29 | 18 | ||
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Aegean Resource Report Resource Website 1+ mentions |
Aegean (RRID:SCR_015965) | data processing software, software application, data analysis software, sequence analysis software, software toolkit, software resource | Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more. | genome, evaluation, annotation, structure, loci |
is listed by: Debian is listed by: OMICtools |
National Science Foundation 1126267 | PMID:22852583 | Free, Available for download, Freely available, | OMICS_19721 | https://github.com/BrendelGroup/AEGeAn, https://sources.debian.org/src/aegean/ | SCR_015965 | AEGeAn: analysis and evaluation of genome annotations, Aegean Toolkit | 2026-08-05 10:46:31 | 6 | |||||
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andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | data processing software, algorithm resource, image analysis software, software application, alignment software, software resource | Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes. | algorithm, computing, estimate, analysis, genome, alignment, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Deutsche Forschungsgemeinschaft Pf672/3-1 | PMID:25504847 | Free, Freely available, Available for download | OMICS_09287, biotools:andi | https://bio.tools/andi, https://sources.debian.org/src/andi/ | SCR_015971 | 2026-08-05 10:46:31 | 41 | ||||||
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Canu Resource Report Resource Website 1000+ mentions |
Canu (RRID:SCR_015880) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). | long-read, assembly, k-mer, weighting, repeat separation, adaptive, pacbio, single-molecule, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Celera assembler |
National Human Genome Research Institute ; US Department of Homeland Security (DHS) HSHQDC-07-C-00020; National Science Foundation NSF IOS-1237993 |
PMID:28298431 DOI:10.1101/071282 |
Free, Available for download | biotools:canu, OMICS_14592 | http://canu.readthedocs.io/en/latest/, https://bio.tools/canu, https://sources.debian.org/src/canu/ | SCR_015880 | 2026-08-05 10:46:30 | 2255 | ||||||
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Baitfisher Resource Report Resource Website 1+ mentions |
Baitfisher (RRID:SCR_015985) | data processing software, image analysis software, software application, alignment software, software toolkit, software resource | Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments. | software, package, multispecies, comparative, genomics, hybrid, enrichment, DNA, probe, design, sequence, alignments |
is listed by: Debian is listed by: OMICtools |
German Research Foundation (DFG) OH81/9-1; NI 1387/1-1; Spanish Ministry of Science and Education (MEC) RYC-2014-15615 |
PMID:27009209 DOI:10.1093/molbev/msw056 |
Free, Available for download | OMICS_11740 | https://sources.debian.org/src/ballview/ | SCR_015985 | 2026-08-05 10:46:31 | 5 | ||||||
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Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | data processing software, software application, data analysis software, sequence analysis software, software toolkit, software resource | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT098051; Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ | SCR_015993 | 2026-08-05 10:46:31 | 51 | |||||
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Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | data processing software, software application, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-08-05 10:46:31 | 568 | |||||||
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HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | data processing software, software application, data analysis software, sequence analysis software, software toolkit, software resource | 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 |
NSF DBI-0096033; NSF DEB-9996118; NIH R01 AI47745; NIH U01 AI43638; 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; NIGMS R01 |
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 | 2026-08-05 10:46:32 | 1497 | |||||
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Indelible Resource Report Resource Website 10+ mentions |
Indelible (RRID:SCR_016163) | software application, simulation software, software resource | Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. | indel, insertion, deletion, biological, sequence, simulation, multi-partitioned, nucleotide, amio-acid, codon, data, set, insertion, deletion, substitution, continous, time, non-homogeneous, non-stationary, phylogeny, simulator, evolution |
is listed by: Debian is listed by: OMICtools |
EPSRC/MRC Doctoral Training Centre studentship ; BBSRC |
PMID:19423664 | Free, Available for download | OMICS_15369 | https://sources.debian.org/src/indelible/ | SCR_016163 | 2026-08-05 10:46:34 | 23 | ||||||
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Fastml Resource Report Resource Website 100+ mentions |
Fastml (RRID:SCR_016092) | software resource, data access protocol, web application, web service | Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences. | ancestral, amino-acid, sequence, reconstruction, phylogenetic, relation, accurate, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Israel Science Foundation 878/09; Bioinformatics Center at Tel-Aviv University |
PMID:22661579 | Free, Freely available | biotools:fastml, OMICS_08650 | https://bio.tools/fastml, https://sources.debian.org/src/fastml/ | SCR_016092 | The FastML Server | 2026-08-05 10:46:33 | 109 |
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