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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | web service, software resource, application programming interface, data access protocol, data or information resource | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | 2026-08-04 09:44:20 | 2 | |||||||
|
ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling. | Protein structure, protein, protein structure refinement, protein structure validation, protein structure prediction, protein structure modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
FWF Austria ; University of Salzburg ; Austria. |
PMID:17517781 | Free, Freely available | biotools:prosa-web | https://bio.tools/prosa-web | SCR_018540 | Protein Structure Analysis web | 2026-08-04 09:44:25 | 104 | |||||
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data processing software, data analysis software, software resource, software application, software toolkit, network analysis software | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | Mutual Information NETworks | 2026-08-04 09:44:22 | 0 | |||||
|
MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, software resource, service resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; NHGRI U01 HG006476; NCI K22 CA188163; NCATS UL1 TR001114; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info, https://bio.tools/mygene.info, https://bio.tools/mygene.info | SCR_018660 | 2026-08-04 09:44:22 | 20 | ||||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, software resource, service resource, web service | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-08-04 09:44:27 | 3 | |||||||
|
TRACESPipe Resource Report Resource Website 1+ mentions |
TRACESPipe (RRID:SCR_018831) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data. | Hybrid pipeline, genome reconstruction, genome analysis, viral genome, host genome, multi organ sequencing, multi organ level, DNA sequence data, multiple organ data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.5524/100771 | Free, Freely available | biotools:tracespipe | http://dx.doi.org/10.5524/100771, https://bio.tools/tracespipe | SCR_018831 | 2026-08-04 09:44:25 | 1 | |||||||
|
D-GENIES Resource Report Resource Website 10+ mentions |
D-GENIES (RRID:SCR_018967) | data processing software, alignment software, standalone software, software resource, software application, image analysis software, web application | Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. | bio.tools |
uses: Minimap2 is listed by: Debian is listed by: bio.tools |
PMID:29888139 | Free, Available for download, Freely available | biotools:d-genies | https://github.com/genotoul-bioinfo/dgenies, https://bio.tools/d-genies | SCR_018967 | Dot plot large GENomes in an Interactive, Efficient and Simple way | 2026-08-04 09:44:26 | 46 | ||||||
|
Robetta Resource Report Resource Website 100+ mentions |
Robetta (RRID:SCR_018805) | analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure. | Protein structure prediction, protein, structure prediction, prediction service, automated prediction, analysis tools, genomic data, protein sequence, protein model, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:15215442 | Restricted | biotools:robetta | https://bio.tools/robetta | SCR_018805 | 2026-08-04 09:44:24 | 330 | |||||||
|
ODAM Resource Report Resource Website 1+ mentions |
ODAM (RRID:SCR_018774) | web service, data management software, software resource, software repository, software application, data access protocol | Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users. | Experimental data tables, research data management, OpenAPI, FAIR Data principles, assessment, EDTMS, data management, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:ODAM, biotools:ODAM | https://bio.tools/ODAM, https://bio.tools/ODAM, https://bio.tools/ODAM, https://bio.tools/ODAM | SCR_018774 | Open Data for Access and Mining | 2026-08-04 09:44:27 | 3 | |||||||
|
AlgPred Resource Report Resource Website 50+ mentions |
AlgPred (RRID:SCR_018780) | data access protocol, software resource, service resource, web service | Web tool for prediction of allergens based on similarity of known epitope with any region of protein. Used for prediction of allergenic proteins and mapping of IgE epitopes. | Allergen prediction, allergenic protein, allergenic protein prediction, IgE epitopes mapping, epitope, protein region, prediction, bio.tools |
is listed by: Debian is listed by: bio.tools |
Council of Scientific and Industrial Research | PMID:16844994 | Free, Freely available | biotools:algpred | https://webs.iiitd.edu.in/raghava/algpred/submission.html, https://bio.tools/algpred | SCR_018780 | 2026-08-04 09:44:24 | 68 | ||||||
|
NanoGalaxy Resource Report Resource Website 1+ mentions |
NanoGalaxy (RRID:SCR_018912) | data processing software, data analysis software, web service, software resource, software application, data access protocol, data visualization software, software toolkit | Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance. | European Galaxy Project, Oxford Nanopore Technologies, Oxford Nanopore Technologies data, data analysis, long reads technology, ONT oriented tools collection, custom Galaxy instance, , Galaxy, Nanopore, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy is related to: University of Freiburg; Baden-Wurttemberg; Germany |
Free, Freely available | biotools:nanogalaxy | https://galaxyproject.org/use/nanogalaxy/, https://bio.tools/nanogalaxy | SCR_018912 | 2026-08-04 09:44:25 | 9 | ||||||||
|
BadMedicine Resource Report Resource Website 1+ mentions |
BadMedicine (RRID:SCR_018879) | code testing framework, software development tool, software resource, software application, software library, software toolkit | Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes. | Electronic Health Record, electronic health record data generation, health data, testing health data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:badmedicine | https://bio.tools/badmedicine | SCR_018879 | 2026-08-04 09:44:25 | 1 | ||||||||
|
ScanITD Resource Report Resource Website 1+ mentions |
ScanITD (RRID:SCR_018886) | data processing software, data analysis software, software resource, sequence analysis software, software application | Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation. | Internal tandem duplication, FLT3, acute myeloid leukemia, TCGA, chimeric alignment, variant allele frequency, variant allele, frequency estimation, , bio.tools |
is listed by: Debian is listed by: bio.tools |
Acute Myeloid Leukemia | DOI:10.5524/100775 | Free, Available for download, Freely available | biotools:ScanItD | https://bio.tools/ScanITD, http://gigadb.org/dataset/100775 | SCR_018886 | Scan Internal Tandem Duplications | 2026-08-04 09:44:25 | 1 | |||||
|
TRiCoLOR Resource Report Resource Website 1+ mentions |
TRiCoLOR (RRID:SCR_018801) | data processing software, data analysis software, software resource, sequence analysis software, software application | Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments. | Tandem repeat, long read sequencing data, whole genome alignment, data analysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tricolor | https://bio.tools/tricolor | SCR_018801 | 2026-08-04 09:44:24 | 2 | ||||||||
|
STAMP Resource Report Resource Website 500+ mentions |
STAMP (RRID:SCR_018887) | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups. | Statistical analysis, taxonomic profile, functional profile, metabolic profile, statistical hypothesis test, plot, sample, sample group, sample pair comparison, bio.tools |
is listed by: Debian is listed by: bio.tools |
Genome Atlantic ; Natural Sciences and Engineering Research Council of Canada ; Australian Research Council ; Canada Foundation for Innovation ; Canada Research Chairs program ; Dalhousie Faculty of Computer Science ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Tula Foundation Killam Trust |
PMID:25061070 | Free, Freely available | biotools:stamp-metagenomic | https://github.com/dparks1134/STAMP, https://github.com/dparks1134/STAMP/releases, https://bio.tools/stamp-metagenomic | SCR_018887 | STAMP v2.1.3, statistical analysis of taxonomic and functional profiles | 2026-08-04 09:44:25 | 504 | |||||
|
E-CRISP Resource Report Resource Website 100+ mentions |
E-CRISP (RRID:SCR_019088) | data access protocol, software resource, web service | Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours. | gRNA sequence design, sgRNA target sequence identification, CRISPR, CRISPR/Cas mediated genome editing, library design, multiple libraries, genome scale libraries, bio.tools |
is listed by: Debian is listed by: bio.tools |
European Research Council Advanced Grant of the European Commission | PMID:24481216 | Free, Freely available | biotools:e-crisp | https://bio.tools/e-crisp | SCR_019088 | 2026-08-04 09:44:28 | 129 | ||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | web service, software resource, data access protocol, database, data or information resource | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-08-04 09:44:30 | 233 | |||||||
|
BiG-SLiCE Resource Report Resource Website 1+ mentions |
BiG-SLiCE (RRID:SCR_019130) | data processing software, software application, software resource, data analysis software | Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data. | Biosynthetic Gene, gene clusters, super linear clustering, clustering data analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Graduate School for Experimental Plant Sciences Netherlands |
DOI:10.1101/2020.08.17.240838 | Free, Available for download, Freely available | biotools:big_slice | https://bio.tools/big_slice | SCR_019130 | Biosynthetic Gene clusters - Super Linear Clustering Engine | 2026-08-04 09:44:29 | 5 | |||||
|
Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | data processing software, data analysis software, software resource, software application, software toolkit | Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data. | structural variants identification, reference genome, structural variant calls generation, whole genome sequencing data, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parliament2 | https://bio.tools/parliament2 | SCR_019187 | 2026-08-04 09:44:33 | 5 | ||||||||
|
epitopepredict Resource Report Resource Website 1+ mentions |
epitopepredict (RRID:SCR_019221) | simulation software, software application, software resource | Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported. | Protein sequence, MHC binding prediction, whole genomes, multiple target MHC allele, epitope prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:epitopepredict | https://epitopepredict.readthedocs.io/en/latest/, https://bio.tools/epitopepredict | SCR_019221 | 2026-08-04 09:44:31 | 2 |
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