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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Crystallography and NMR System (CNS) Resource Report Resource Website 1+ mentions |
Crystallography and NMR System (CNS) (RRID:SCR_014223) | CNS | data processing software, software application, data visualization software, software toolkit, software resource | Software designed to provide a multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Features include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. Modules, libraries, utility programs, tutorials, and a syntax manual are available on the website. | structure determination, software suite, macromolecular structure determination, data visualization software, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Yale University; Connecticut; USA |
PMID:9757107 | Available to academic institutions, Request form must be submitted | biotools:cnssolve | https://bio.tools/cnssolve | SCR_014223 | Crystallography and NMR System | 2026-08-05 10:46:08 | 8 | |||||
|
ImageMagick Resource Report Resource Website 100+ mentions |
ImageMagick (RRID:SCR_014491) | data processing software, software application, software resource, image processing software | Software suite for creating, editing, composing, and converting bitmap images. It can read and write images in over 200 formats including PNG, JPEG, JPEG-2000, GIF, TIFF, DPX, EXR, WebP, Postscript, PDF, and SVG. The user can use this software to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves. | image editing, image processing software, image analysis software, bitmap, adjust image colors, bezier curves | is listed by: Debian | Restricted | https://sources.debian.org/src/imagemagick/ | SCR_014491 | 2026-08-05 10:46:07 | 133 | |||||||||
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | software resource, data processing software, software application, data analysis software | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-08-05 10:46:09 | 3702 | |||||
|
Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | 2026-08-05 10:46:11 | 8838 | |||||||
|
SPEX2 Resource Report Resource Website 1+ mentions |
SPEX2 (RRID:SCR_014923) | data processing software, software application, sequence analysis software, data analysis software, 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 | 2026-08-05 10:46:13 | 1 | ||||||||
|
RepeatScout Resource Report Resource Website 500+ mentions |
RepeatScout (RRID:SCR_014653) | data processing software, algorithm resource, software application, data analysis software, sequence analysis software, software resource | Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | algorithm, sequence analysis, repeat, genome sequence, de novo, repeat family, repeat library, bio.tools |
is used by: RepeatModeler is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:15961478 | THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:RepeatScout, biotools:RepeatScout | https://bio.tools/RepeatScout, https://bio.tools/RepeatScout, https://bio.tools/RepeatScout | SCR_014653 | 2026-08-05 10:46:10 | 815 | |||||||
|
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, wiki, narrative resource | 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 | Online Resource for Community Annotation of Eukaryotes (OrcAE) | 2026-08-05 10:46:14 | 16 | |||||
|
libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | software application, simulation software, software resource | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | 2026-08-05 10:46:12 | 11 | ||||||
|
Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | 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 tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, prokaryote, genome, prokaryotic genome, sequence analysis software, annotation software, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04220, biotools:prokka | https://bio.tools/prokka, https://sources.debian.org/src/prokka/, https://sources.debian.org/src/prokka/ | SCR_014732 | 2026-08-05 10:46:11 | 4876 | |||||||
|
MeroX Resource Report Resource Website 50+ mentions |
MeroX (RRID:SCR_014956) | data processing software, software application, sequence analysis software, data analysis software, 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 | 2026-08-05 10:46:15 | 74 | |||||||
|
Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | data management software, software application, software resource, data analysis service, production service resource, 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 | 2026-08-05 10:46:38 | 2 | |||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data processing software, software application, data visualization software, data analysis software, standalone software, software resource, 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 | 2026-08-05 10:46:36 | 143 | ||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data processing software, web application, software application, data analysis software, sequence analysis software, software resource | 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 | 2026-08-05 10:46:36 | 4 | ||||
|
TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | data or information resource, data repository, portal, consortium, disease-related portal, topical portal, organization portal, storage service resource, service resource | Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data. | collect, data, sharing, analysis, tuberculosis, global, bio.tools |
is listed by: NIAID is listed by: bio.tools is listed by: Debian |
tuberculosis | NIH | DOI:10.1128/JCM.01013-17 | Free, Freely available | r3d100013925, biotools:TB_Portals | https://bio.tools/TB_Portals, https://doi.org/10.17616/R31NJN8L | SCR_016594 | 2026-08-05 10:46:41 | 12 | |||||
|
Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | data processing software, software application, data analysis software, sequence analysis software, software resource, data analytics software | Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. | gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF 1640775 | Free, Available for download, Freely available | biotools:Libra_k-mer | https://bio.tools/Libra_k-mer | SCR_016608 | 2026-08-05 10:46:37 | 0 | |||||||
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MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | data processing software, software application, sequence analysis software, data analysis software, software resource | 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 | 2026-08-05 10:46:39 | 8 | ||||||
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cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | data processing software, software application, software resource, image 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 | 2026-08-05 10:46:35 | 64 | ||||
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kallisto Resource Report Resource Website 100+ mentions |
kallisto (RRID:SCR_016582) | software resource, data processing software, software application, data analysis software | Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads. | bio.tools |
is listed by: Debian is listed by: bio.tools works with: sleuth works with: kb_python |
PMID:27043002 | Free, Available for download, Freely available | biotools:kallisto | https://pachterlab.github.io/kallisto/download.html, https://bio.tools/kallisto, https://sources.debian.org/src/kallisto/ | SCR_016582 | kallisto v0.43.1 | 2026-08-05 10:46:36 | 127 | ||||||
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Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | web application, software resource, data analysis service, production service resource, service resource, analysis service resource | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | 2026-08-05 10:46:43 | 22 | ||||||
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Centrifuge Classifier Resource Report Resource Website 1+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers. | classification, large, metagenomic, sequence, DNA, microbial, sample, analysis, data, desktop, computer, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Pavian has parent organization: Center for Computational Biology at JHU |
U. S. Army Research Office W911NF1410490; NSF ABI1356078; NHGRI R01 HG006677; NIGMS R01 GM083873 |
DOI:10.1101/gr.210641.116 | Free, Available for download, Freely available | biotools:centrifuge, OMICS_12217 | https://github.com/infphilo/centrifuge, https://bio.tools/centrifuge, https://sources.debian.org/src/centrifuge/ | SCR_016665 | 2026-08-05 10:46:43 | 9 |
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