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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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InterEvol database Resource Report Resource Website 10+ mentions |
InterEvol database (RRID:SCR_006054) | InterEvol | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface | structure, evolution, protein complex, interface, protein complex, sequence alignment, plug in, protein structure, visualization, pymol plugin, structural homolog, structural interolog, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: CEA; Gif sur Yvette; France |
Commissariat a lEnergie Atomique ; ANR HPGenVar |
PMID:22053089 | Free and open to all users - no login requirement | nlx_151453, biotools:interevol | https://bio.tools/interevol | SCR_006054 | SciCrunch Registry | 2026-10-10 12:37:24 | 10 | |||||
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RAxML Resource Report Resource Website 10000+ mentions |
RAxML (RRID:SCR_006086) | RAxML | data analysis software, data processing software, software application, software resource | Software program for phylogenetic analyses of large datasets under maximum likelihood. | phylogeny, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: RAxML Next Generation works with: PAML |
PMID:24451623 PMID:16928733 PMID:15608047 DOI:10.1093/bioinformatics/btu033 |
GNU General Public License | biotools:raxml, OMICS_02242 | https://bio.tools/raxml, https://sources.debian.org/src/raxml/ | SCR_006086 | SciCrunch Registry | Randomized Axelerated Maximum Likelihood | 2026-10-10 12:37:17 | 12997 | |||||
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bioRxiv Resource Report Resource Website 1000+ mentions |
bioRxiv (RRID:SCR_003933) | bioRxiv | community building portal, data or information resource, database, portal | A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version. | preprint, life science, bio.tools, FASEB list |
is used by: PrePubMed is listed by: LabWorm is listed by: bio.tools is listed by: Debian is related to: Overleaf has parent organization: Cold Spring Harbor Laboratory |
Free, Acknowledgement requested, The community can contribute to this resource | biotools:bioRxiv, nlx_158302 | https://bio.tools/bioRxiv | SCR_003933 | SciCrunch Registry | bioRxiv - the preprint server for biology | 2026-10-10 12:36:55 | 1368 | ||||||
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Git Resource Report Resource Website 50+ mentions |
Git (RRID:SCR_003932) | software application, software development tool, software resource, version source control system | A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows. | version control, distributed, bio.tools |
is used by: DataLad is used by: G-Node Data Infrastructure Services is listed by: bio.tools is listed by: Debian works with: git-annex |
GNU General Public License, v2 | nlx_158301, biotools:Git | https://bio.tools/Git | SCR_003932 | SciCrunch Registry | 2026-10-10 12:36:57 | 73 | ||||||||
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Quantitative Enrichment of Sequence Tags Resource Report Resource Website 10+ mentions |
Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) | QuEST | software resource | A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments. | genome-wide, transcription factor binding site, chip-seq, transcription factor, binding site, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Stanford University; Stanford; California |
PMID:19160518 | OMICS_00458, biotools:quest | https://bio.tools/quest | SCR_004065 | SciCrunch Registry | Quantitative Enrichment of Sequence Tags: QuEST | 2026-10-10 12:36:57 | 49 | ||||||
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Pash 3.0 Resource Report Resource Website 1+ mentions |
Pash 3.0 (RRID:SCR_004078) | Pash 3.0 | software resource | Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21092284 | biotools:pash, OMICS_00586 | https://bio.tools/pash | SCR_004078 | SciCrunch Registry | 2026-10-10 12:36:58 | 1 | |||||||
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EpiGRAPH Resource Report Resource Website 10+ mentions |
EpiGRAPH (RRID:SCR_004326) | EpiGRAPH | software resource | A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00633, biotools:epigraph | https://bio.tools/epigraph | SCR_004326 | SciCrunch Registry | 2026-10-10 12:36:52 | 18 | |||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, data repository, database, service resource, storage service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | SciCrunch Registry | 2026-10-10 12:37:00 | 15598 | ||||||
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InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | SciCrunch Registry | 2026-10-10 12:36:49 | 0 | ||||||
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bcbio-nextgen Resource Report Resource Website 100+ mentions |
bcbio-nextgen (RRID:SCR_004316) | bcbio-nextgen | software resource | A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:bcbio-nextgen, OMICS_01121, BioTools:bcbio-nextgen | https://github.com/chapmanb/bcbb/blob/master/nextgen/README.md, https://bio.tools/bcbio-nextgen, https://bio.tools/bcbio-nextgen | SCR_004316 | SciCrunch Registry | 2026-10-10 12:36:52 | 165 | |||||||
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PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions |
PDBe - Protein Data Bank in Europe (RRID:SCR_004312) | PDBe | data or information resource, data repository, database, service resource, storage service resource | The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules. | x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, 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: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline |
European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4 |
PMID:21045060 PMID:21460450 PMID:19858099 |
r3d100012791, biotools:pdbe, nlx_32372 | https://bio.tools/pdbe, https://doi.org/10.17616/R3J226 | SCR_004312 | SciCrunch Registry | Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database | 2026-10-10 12:37:08 | 55 | |||||
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NeuroMatic Resource Report Resource Website 100+ mentions |
NeuroMatic (RRID:SCR_004186) | data analysis software, data processing software, software application, software resource | NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC | epsc, epsp, event, fit, acquisition, data management, ipsc, ipsp, nclamp, software, spike, spike train, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
PMID:29670519 | nif-0000-00073, biotools:neuromatic | https://bio.tools/neuromatic | SCR_004186 | SciCrunch Registry | NeuroMatic | 2026-10-10 12:37:06 | 315 | |||||||
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TagDust Resource Report Resource Website 50+ mentions |
TagDust (RRID:SCR_004175) | TagDust | software resource | A program to eliminate artifactual reads from next-generation sequencing data sets. | unix/linux, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:19737799 | biotools:tagdust, OMICS_01095, biotools:nexalign | https://bio.tools/tagdust, https://bio.tools/nexalign | SCR_004175 | SciCrunch Registry | 2026-10-10 12:36:49 | 55 | |||||||
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RatMine Resource Report Resource Website 1+ mentions |
RatMine (RRID:SCR_004190) | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | RatMine integrates data from RGD, UniProtKB, NCBI, KEGG and other sources to form a web-based data warehouse and tool set tailored for rat based data research. Search RatMine by entering names, identifiers, or keywords for genes, proteins, pathways, papers, etc. Additionally, we support programmatic access to our data through Application Programming Interface - choose from Perl or Java API. RatMine is a data warehouse that integrates many diverse biological data sets. The main focus is R. norvegicus genomics and proteomics. By integrating such data into one place it is possible to construct queries across domains of biological knowledge. The RatMine user interface is designed to go beyond simply looking up an identifier and viewing a report page. Some of the features include: * Quick Search is available just like on other sites, type in an identifier to see a report page. * Template queries are ''canned'' queries that provide a simple form to perform a specific task. You can create your own templates if you log in. * Lists lets you operate on whole lists of data at once. You can upload lists or save them from results tables. We also create useful public lists for everyone to use. * MyMine lets you create an account to save your own queries, bags and templates, as well as marking public templates as favorites. | disease, interaction, proteins, single nucleotide, gene ontology, mammalian phenotype, publication, genomics, pathway, quantitative trait loci, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Medical College of Wisconsin; Wisconsin; USA |
biotools:RatMine, nlx_21635 | https://bio.tools/RatMine | SCR_004190 | SciCrunch Registry | 2026-10-10 12:36:44 | 5 | |||||||||
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Artemis: Genome Browser and Annotation Tool Resource Report Resource Website 100+ mentions |
Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) | Artemis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | training tool, genome browser, gene annotation, java, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: DNAPlotter has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom works with: Alien-hunter |
Wellcome Trust | PMID:11120685 DOI:10.1093/bioinformatics/btr703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_28554, OMICS_00903, biotools:artemis | https://bio.tools/artemis, https://sources.debian.org/src/art-nextgen-simulation-tools/ | SCR_004267 | SciCrunch Registry | 2026-10-10 12:37:08 | 422 | |||||
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DER Finder Resource Report Resource Website 1+ mentions |
DER Finder (RRID:SCR_004250) | DER Finder | data processing software, software application, software library, software resource, software toolkit | R package for differential expression analysis of RNA-seq data. | differential expression, rna-seq, false discovery rate, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24398039 | Free, Public | biotools:derfinder, OMICS_02208 | https://bio.tools/derfinder | SCR_004250 | SciCrunch Registry | derfinder | 2026-10-10 12:36:45 | 5 | |||||
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Stem Cell Discovery Engine Resource Report Resource Website 50+ mentions |
Stem Cell Discovery Engine (RRID:SCR_004453) | SCDE | analysis service resource, data or information resource, data repository, database, production service resource, service resource, software resource, source code, storage service resource | An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket. | stem cell, analysis, cancer stem cell, galaxy, gene, pathway, molecular signature, tissue, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard T.H. Chan School of Public Health |
Cancer | NCI 1RC2CA148222-01 | PMID:22121217 | Free, The community can contribute to this resource | biotools:scde_discovery, nlx_44656 | https://bio.tools/scde_discovery | SCR_004453 | SciCrunch Registry | Harvard Stem Cell Discovery Engine, SCDE - Stem Cell Discovery Engine | 2026-10-10 12:37:02 | 57 | |||
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Kdetrees Resource Report Resource Website |
Kdetrees (RRID:SCR_004522) | software resource | R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. | applet, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24764459 | GNU General Public License, v2 | biotools:kdetrees, OMICS_04172 | https://github.com/grady/kdetrees, https://bio.tools/kdetrees | SCR_004522 | SciCrunch Registry | kdetrees: Nonparametric method for identifying discordant phylogenetic trees | 2026-10-10 12:37:14 | 0 | ||||||
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SnoopCGH Resource Report Resource Website 1+ mentions |
SnoopCGH (RRID:SCR_004420) | SnoopCGH | software resource | A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:19687029 | biotools:snoopcgh, OMICS_00736 | https://bio.tools/snoopcgh | SCR_004420 | SciCrunch Registry | 2026-10-10 12:36:54 | 2 | |||||||
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GASSST Resource Report Resource Website 1+ mentions |
GASSST (RRID:SCR_004413) | GASSST | software resource | Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Rennes 1; Rennes; France |
PMID:20739310 | CeCILL license, v2 | biotools:gassst, OMICS_00663 | https://bio.tools/gassst | SCR_004413 | SciCrunch Registry | GASSST : Global Alignment Short Sequence Search Tool, Global Alignment Short Sequence Search Tool | 2026-10-10 12:36:54 | 7 |
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
