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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | data processing software, algorithm resource, software resource, image analysis software, alignment software, software application | 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 | 2026-07-30 09:29:58 | 41 | ||||||
|
DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | data processing software, sequence analysis software, data analysis software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
EU STREP APrIL II contract no. FP6-508861; EU NoE BIOPATTERN contract no. FP6-508803; Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind, https://sources.debian.org/src/disulfinder/ | SCR_016072 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-07-30 09:30:06 | 66 | ||||
|
SC3 Resource Report Resource Website 10+ mentions |
SC3 (RRID:SCR_015953) | data processing software, sequence analysis software, data analysis software, software resource, software application | Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients. | scRNA-seq, interactive, cluster, clustering, cell, single, rna, rnaseq, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust 104710/Z/14/Z; Belgian Network DYSCO ; FRS-FNRS ; Belgian State Science Policy Office ; ARC (Action de Recherche Concerte) ; Wallonia-Brussels Federation ; EPSRC EP/N014529/1; Sanger Institute ; University of Edinburgh ; Bloodwise 13003; MRC ; Kay Kendall Leukaemia Fund ; Cambridge NIHR Biomedical Research Center ; Cambridge Experimental Cancer Medicine Centre ; Leukemia and Lymphoma Society of America 07037 |
PMID:28346451 | Free, Available for download | biotools:sc3 | https://bio.tools/sc3 | SCR_015953 | SC3 package, Single-Cell Consensus Clustering | 2026-07-30 09:29:48 | 20 | |||||
|
Exonerate Resource Report Resource Website 100+ mentions |
Exonerate (RRID:SCR_016088) | data processing software, software toolkit, software resource, image analysis software, alignment software, software application | Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence, alignment, pairwise, comparison, dynamic, programming, heuristic, bio.tools |
is used by: ExonerateTransferAnnotation is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:15713233 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:exonerate | https://bio.tools/exonerate | SCR_016088 | 2026-07-30 09:30:06 | 374 | |||||||
|
Bio++ Resource Report Resource Website 50+ mentions |
Bio++ (RRID:SCR_016055) | software toolkit, software resource, software library, software development tool, software application | Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic, molecular evolution, genetic, program, write, tool, visualize, edit, print, data, bioinformatic, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15696, biotools:biopp | https://sources.debian.org/src/bppsuite/, https://groups.google.com/forum/#!categories/biopp-help-forum/all-questions, https://github.com/BioPP, https://bio.tools/biopp, | SCR_016055 | Bppsuite, Bppphyview, Bio++ program suite, Bio++ Phylogenetic Viewer | 2026-07-30 09:29:51 | 65 | |||||||
|
EnrichmentMap Resource Report Resource Website 500+ mentions |
EnrichmentMap (RRID:SCR_016052) | data processing software, source code, data visualization software, software resource, software application | Source code of a Cytoscape plugin for functional enrichment visualization. It organizes gene-sets, such as pathways and Gene Ontology terms, into a network to reveal which mutually overlapping gene-sets cluster together. | cytoscape, functional, visualization, enrichment, gene, mapping, genome, pathway, network, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: Cytoscape |
NHGRI P41 HG04118; Ontario Genomics Institute ; Heart and Stroke Foundation of Canada ; Canada Foundation for Innovation ; Ontario Research Fund (ORF) |
PMID:21085593 | biotools:enrichmentmap | https://github.com/BaderLab/EnrichmentMapApp, https://bio.tools/enrichmentmap | SCR_016052 | 2026-07-30 09:29:51 | 545 | |||||||
|
Necklace Resource Report Resource Website 1+ mentions |
Necklace (RRID:SCR_016103) | data processing software, software resource, image analysis software, alignment software, software application | Software that combines reference and assembled transcriptomes for RNA-Seq analysis. It replaces many manual steps in the pipeline of RNA-Seq analyses involving species with incomplete genome or annotations. | RNA, Transcriptome, Non-model species, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:28836999 | Free, Available for download | biotools:necklace | https://bio.tools/necklace | SCR_016103 | Lace software | 2026-07-30 09:29:52 | 3 | ||||||
|
BLINK Resource Report Resource Website 1+ mentions |
BLINK (RRID:SCR_016288) | data processing software, algorithm resource, data analysis software, software resource, software application | Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power. | GWAS, SNP, dataset, r, genome, bayesian, linkage, nested, keyway, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Tutorial available | biotools:BLINK | https://bio.tools/BLINK | SCR_016288 | BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) | 2026-07-30 09:30:01 | 1 | |||||||
|
HyPhy Resource Report Resource Website 1000+ mentions |
HyPhy (RRID:SCR_016162) | data processing software, sequence analysis software, software toolkit, data analysis software, software resource, software application | 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 | 2026-07-30 09:30:07 | 1497 | |||||
|
zUMIs Resource Report Resource Website 100+ mentions |
zUMIs (RRID:SCR_016139) | data processing software, software application, data analysis software, software resource | Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information. | single-cell, RNA-seq, UMI, Genomics, shell, r, perl, rna, cdna, cell, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/153940 | Open source, Free, Available for download | biotools:zumis | https://bio.tools/zumis | SCR_016139 | zumi | 2026-07-30 09:29:59 | 118 | ||||||
|
BioPlex Resource Report Resource Website 1000+ mentions |
BioPlex (RRID:SCR_016144) | service resource, data repository, data or information resource, database, storage service resource | Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection. | cell, line, protein, immunopurification, mass, spectrometry, interaction, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Harvard Medical School; Massachusetts; USA |
NHGRI U41HG006673; NIDDK K01 DK098285; Canadian Institutes for Health Research |
PMID:28514442 | biotools:bioplex_2.0 | https://bio.tools/bioplex_2.0 | SCR_016144 | BioPlex (biophysical interactions of ORFeome-based complexes), Harvard BioPlex, Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX) | 2026-07-30 09:29:59 | 1355 | ||||||
|
mentha Resource Report Resource Website 100+ mentions |
mentha (RRID:SCR_016148) | data processing software, web application, data analysis software, software resource, data or information resource, software application, database | Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. | protein, ppi, imex, interactome, archival, bio.tools, FASEB list |
uses: PSICQUIC Registry is listed by: Debian is listed by: bio.tools is related to: IMEx - The International Molecular Exchange Consortium |
PMID:23900247 | biotools:mentha, r3d100011124 | https://bio.tools/mentha, https://doi.org/10.17616/R3SP8V | SCR_016148 | 2026-07-30 09:29:59 | 149 | ||||||||
|
FluxModeCalculator Resource Report Resource Website 1+ mentions |
FluxModeCalculator (RRID:SCR_016290) | data processing software, software application, data analysis software, software resource | Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | efm, flux, stoichiometry, algorithm, matlab, linux, model, magnitude, bio.tools |
is listed by: Debian is listed by: bio.tools |
Netherlands Consortium for Systems Biology (NCSB) ; Center of Medical Systems Biology (CMSB) ; European Network for Genetic and Genomic Epidemiology (ENGAGE) ; Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) ; CardioVascular Research Netherlands (CVON-ENERGISE) |
PMID:26685305 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fluxmodecalculator, OMICS_10894 | https://bio.tools/fluxmodecalculator | SCR_016290 | Flux Mode Calculator | 2026-07-30 09:30:08 | 1 | |||||
|
Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | data management software, service resource, data analysis service, software resource, software application, production service resource, analysis service resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-07-30 09:30:02 | 2 | |||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data processing software, software toolkit, data analysis software, software resource, software application | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-07-30 09:30:09 | 5 | |||||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data processing software, sequence analysis software, web application, data analysis software, software resource, software application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-07-30 09:30:10 | 4 | ||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data processing software, software toolkit, data analysis software, software resource, software application | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-07-30 09:30:09 | 2 | |||||
|
MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | data processing software, sequence analysis software, data analysis software, software resource, software application | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-07-30 09:30:10 | 8 | ||||||
|
cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | software resource, software application, image processing software, data processing software | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | computational imaging system for Transmission Electron Microscopy | 2026-07-30 09:30:10 | 64 | ||||
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Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data processing software, data analysis software, data visualization software, software resource, standalone software, software application, image processing software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | MIB, Microscopy Image Browser | 2026-07-30 09:30:04 | 143 |
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