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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DARC - Database for Aligned Ribosomal Complexes Resource Report Resource Website 10+ mentions |
DARC - Database for Aligned Ribosomal Complexes (RRID:SCR_006932) | DARC | analysis service resource, data analysis service, data or information resource, database, model, production service resource, service resource | A database for aligned ribosomal complexes that provides a resource for directly comparing the structures. A collection of files deposited in the RCSB protein data bank and the Electron Microscopy Data Bank have been aligned so as to make direct comparison of the structures possible. An easy-to-use, searchable interface allows users to access and download >130 cryo-EM maps and >300 atomic models in the format of brix and pdb files, respectively. The aligned coordinate system substantially simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors. | ribosomal complex, cryo-electron microscopy, ribosomal particle, atomic model, ribosome, x-ray crystallography, structure, bio.tools |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Electron Microscopy Data Bank at PDBe (MSD-EBI) is listed by: Debian is listed by: bio.tools has parent organization: Ludwig-Maximilians-University; Munich; Germany |
DFG SFB594; DFG SFB646; DFG WI3285/1-1 |
PMID:22009674 | biotools:darc_site, nlx_149452 | https://bio.tools/darc_site | SCR_006932 | SciCrunch Registry | The DARC site, Database for Aligned Ribosomal Complexes, Database for Aligned Ribosomal Complexes (DARC), DARC site | 2026-11-07 12:00:47 | 27 | |||||
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HTSeq Resource Report Resource Website 5000+ mentions |
HTSeq (RRID:SCR_005514) | HTSeq | authoring tool, data processing software, software application, software resource, standalone software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge. | python, high-throughput sequencing assay, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
DOI:10.1093/bioinformatics/btu638 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:htseq, OMICS_01053 | https://bio.tools/htseq | http://www-huber.embl.de/users/anders/HTSeq/, https://sources.debian.org/src/python3-htseq/ | SCR_005514 | SciCrunch Registry | HTSeq: Analysing high-throughput sequencing data with Python | 2026-11-07 12:00:46 | 8618 | ||||
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GeneTalk Resource Report Resource Website 10+ mentions |
GeneTalk (RRID:SCR_005231) | GeneTalk | blog, community building portal, data or information resource, data repository, database, narrative resource, portal, service resource, storage service resource | A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. VCFs (Variant Call Formats) are preprocessed and annotated, you can filter them, access all databases and provide your expertise to the community by creating annotations. | sequence variant, annotation, exome sequencing, genetic variant, gene, data sharing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22826540 | The community can contribute to this resource, Free, (during beta period) | OMICS_00270, biotools:genetalk | https://bio.tools/genetalk | SCR_005231 | SciCrunch Registry | GeneTalk - The Professional Network and Online Tool for Geneticists | 2026-11-07 12:00:46 | 31 | |||||
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SPM Resource Report Resource Website 5000+ mentions Issue |
SPM (RRID:SCR_007037) | SPM | data analysis software, data processing software, image analysis software, software application, software resource | Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG. | analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEG, bio.tools |
uses: Neuroimaging Data Model uses: imcalc: SPM batch image calculator is used by: rsfMRI_fconn calculation is used by: Automatic Analysis is used by: auto_acpc_reorient is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite is affiliated with: Clinical Toolbox for SPM is affiliated with: Statistical non-Parametric Mapping is related to: WFU Biological Parametric Mapping Toolbox is related to: vis: SPM Visualized Statistics toolbox is related to: LEAD-DBS is related to: CCHMC Pediatric Brain Templates is related to: IBMA toolbox is related to: ArtRepair for robust fMRI is related to: ASL data processing tool box is related to: BrainVISA / Anatomist is related to: MRIcro Software is related to: xjView: A Viewing Program For SPM is related to: BrainMagix SPM Viewer is related to: MarsBaR region of interest toolbox for SPM is related to: NIRS-SPM is related to: SPM SS - fMRI functional localizers is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: Dementia-specific FDG PET Template for SPM analyses is related to: SPM Anatomy Toolbox is related to: MIPAV: Medical Image Processing and Visualization is related to: MATLAB is related to: hMRI-toolbox is related to: Sandwich Estimator Toolbox has parent organization: University College London; London; United Kingdom is required by: MRTool provides: TSDiffAna has plug in: ICN_Atlas works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: NIAG Addiction Data works with: ICN_Atlas works with: spm_auto_reorient_coregister works with: Computational Anatomy Toolbox for SPM works with: FieldTrip works with: POAS4SPM |
Free, Available for download, Freely available | biotools:SPM | https://github.com/spm/spm12, https://bio.tools/SPM | https://www.fil.ion.ucl.ac.uk/spm/ | SCR_007037 | SciCrunch Registry | Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 | 2026-11-07 12:00:37 | 8748 | |||||
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MUSCLE Resource Report Resource Website 10000+ mentions |
MUSCLE (RRID:SCR_011812) | MUSCLE | alignment software, analysis service resource, data analysis service, data analysis software, data processing software, image analysis software, production service resource, service resource, software application, software resource | Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation. | bio.tools |
is used by: TranslatorX is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: PREFAB has parent organization: European Bioinformatics Institute |
PMID:15034147 PMID:15318951 DOI:10.1093/nar/gkh340 |
biotools:muscle, OMICS_00982 | https://bio.tools/muscle, http://www.drive5.com/muscle/, https://www.drive5.com/muscle/manual/, https://www.drive5, http://bioconductor.org/packages/release/bioc/html/muscle.html.com/muscle/manual/install.html, https://sources.debian.org/src/muscle/ | SCR_011812 | SciCrunch Registry | MUltiple Sequence Comparison by Log- Expectation | 2026-11-07 12:00:49 | 17169 | ||||||
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neXtProt Resource Report Resource Website 100+ mentions |
neXtProt (RRID:SCR_008911) | data or information resource, database, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2025. Human protein knowledge platform. Knowledge platform for human proteins selects and filters high throughput data pertinent to human proteins from UniProtKB. Extends UniProtKB/Swiss-Prot annotations for human proteins to include several new data types. | Protein, proteomics, sirna, 3d, pathway, variant, protein-protein interaction, protein-drug interaction, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: UniProtKB has parent organization: SIB Swiss Institute of Bioinformatics |
SIB ; Swiss Commission for Technology and Innovation |
PMID:22139911 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:nextprot, nlx_151482 | https://bio.tools/nextprot | SCR_008911 | SciCrunch Registry | 2026-11-07 12:00:48 | 177 | ||||||
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Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology Resource Report Resource Website 1000+ mentions |
Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) | data acquisition software, data or information resource, data processing software, database, software application, software resource | Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013. | function, gene, bioinformatics, data, database, human, meta search engine, prediction, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Karlsruhe Institute of Technology; Karlsruhe; Germany |
biotools:harvester, nif-0000-10169 | https://bio.tools/harvester | SCR_008017 | SciCrunch Registry | Harvester IV | 2026-11-07 12:00:34 | 1480 | ||||||||
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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 | SciCrunch Registry | PLEXdb - Gene expression resources for plants and plant pathogens, Plant Expression Database | 2026-11-07 12:00:34 | 21 | |||||
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PASA Resource Report Resource Website 1000+ mentions |
PASA (RRID:SCR_014656) | data analysis software, data processing software, sequence analysis software, software application, software resource | Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute. | gene structure, annotation, gene structure analysis tool, spliced alignment, transcript sequence, bio.tools |
is used by: BRO_annotation is listed by: Debian is listed by: bio.tools |
DOI:10.1093/nar/gkg770 | Available for download | biotools:PASA | https://bio.tools/PASA | SCR_014656 | SciCrunch Registry | Program to Assemble Spliced Alignments (PASA), Program to Assemble Spliced Alignments | 2026-11-07 12:00:44 | 1123 | ||||||
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Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | data processing software, software application, software resource, workflow software | A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. | workflow, MD, molecular dynamics, simulation, software, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: bioKepler has parent organization: University of California at San Diego; California; USA |
NIGMS P41GM103426 | Requires Linux | biotools:ambergpumdsimulation | http://nbcr.ucsd.edu/data/downloads/workflows/, https://bio.tools/ambergpumdsimulation | SCR_014389 | SciCrunch Registry | Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation | 2026-11-07 12:00:44 | 1 | ||||||
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software application, software library, software resource, software toolkit | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | SciCrunch Registry | 2026-11-07 12:00:18 | 77 | ||||||||
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SPEX2 Resource Report Resource Website 1+ mentions |
SPEX2 (RRID:SCR_014923) | data analysis software, data processing software, sequence analysis software, software application, software resource | Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns. | software, spatial gene expression, fly, embryo, extraction, mrna, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Carnegie Mellon University; Pennsylvania; USA |
PMID:20529936 | biotools:spex2 | https://bio.tools/spex2 | SCR_014923 | SciCrunch Registry | 2026-11-07 11:58:19 | 1 | ||||||||
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DOGMA Resource Report Resource Website 100+ mentions |
DOGMA (RRID:SCR_015060) | software resource, web application | Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes. | chloroplast, mitochondria, genome annotation, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:15180927 | Freely available | biotools:DOGMA | https://bio.tools/DOGMA | SCR_015060 | SciCrunch Registry | Dual Organellar GenoMe Annotator, Dual Organellar GenoMe Annotator (DOGMA) | 2026-11-07 11:57:59 | 428 | ||||||
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Online Resource for Community Annotation of Eukaryotes Resource Report Resource Website 10+ mentions |
Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) | OrcAE, ORCAE | data or information resource, narrative resource, wiki | Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community. | genome annotation, gene validation, community driven, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Bioinformatics Gent has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:23132114 | Free, Account required, The research community can contribute to this resource | biotools:orcae | https://bio.tools/orcae | SCR_014989 | SciCrunch Registry | Online Resource for Community Annotation of Eukaryotes (OrcAE) | 2026-11-07 11:58:23 | 17 | |||||
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SeaView Resource Report Resource Website 1000+ mentions |
SeaView (RRID:SCR_015059) | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource | Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees. | sequence alignment, molecular phylogeny, phylogenetic tree, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:19854763 DOI:10.1093/molbev/msp259 |
Free, Available for download | OMICS_08908, biotools:seaview | https://bio.tools/seaview, https://sources.debian.org/src/seaview/ | SCR_015059 | SciCrunch Registry | 2026-11-07 11:58:22 | 1817 | |||||||
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MeroX Resource Report Resource Website 50+ mentions |
MeroX (RRID:SCR_014956) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links. | sequence analysis software, cross linking, mass spectrometry, MS cleavage, fragmentation, cleavable cross link, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: StavroX |
PMID:25261217 | THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:MeroX, biotools:MeroX | https://bio.tools/MeroX, https://bio.tools/MeroX, https://bio.tools/MeroX | SCR_014956 | SciCrunch Registry | 2026-11-07 11:58:23 | 74 | |||||||
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BUSCO Resource Report Resource Website 5000+ mentions |
BUSCO (RRID:SCR_015008) | algorithm resource, data analysis software, data processing software, software application, software resource | Software tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. | genome assembly, annotation completeness, quantitative method, bio.tools |
is used by: rnaQUAST is recommended by: CEGMA is listed by: Debian is listed by: bio.tools is related to: CEGMA works with: BUSCOMP |
Marie Curie International Outgoing Fellowship ; Swiss National Science Foundation |
DOI:10.1093/bioinformatics/btv351 | Free, Available for download, Freely available | biotools:busco | https://gitlab.com/ezlab/busco, https://bio.tools/busco, https://sources.debian.org/src/busco/ | SCR_015008 | SciCrunch Registry | BUSCO v2, Benchmarking Universal Single-Copy Orthologs (BUSCO), Benchmarking Universal Single-Copy Orthologs, BUSCO v1 | 2026-11-07 11:58:07 | 8320 | |||||
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LTR_Finder Resource Report Resource Website 500+ mentions |
LTR_Finder (RRID:SCR_015247) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web software capable of scanning large-scale sequences for full-length LTR retrotranspsons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Long Terminal Repeat retrotransposons, Long Terminal Repeat, retrotransposon prediction, genome sequences, LTR prediction, LTR structure prediction, DNA sequence, biotools |
is listed by: Debian is listed by: bio.tools |
Fudan University ; Shanghai ; China |
PMID:17485477 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_020944, biotools:ltr_finder | https://bio.tools/ltr_finder | SCR_015247 | SciCrunch Registry | LTR Finder | 2026-11-07 11:58:24 | 807 | |||||
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HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2, https://bio.tools/hisat2, https://sources.debian.org/src/hisat2/ | SCR_015530 | SciCrunch Registry | HISAT | 2026-11-07 11:58:27 | 20753 | |||||
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primers4clades Resource Report Resource Website 1+ mentions |
primers4clades (RRID:SCR_015714) | software resource, web application | Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs. | pcr primer, metagenomic dna, phylogenetic lineage, primer, clade, bio.tools |
is listed by: Debian is listed by: bio.tools |
DGAPA IN201806-2; CONACyT-Mexico P1-60071; CSIC 200720I038 |
PMID:19465390 | Freely available, Free for academic use, Tutorial available | biotools:primers4clades | http://maya.ccg.unam.mx/primers4clades, https://bio.tools/primers4clades | SCR_015714 | SciCrunch Registry | 2026-11-07 11:58:14 | 2 |
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