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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | data processing software, software application, software resource, 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 | 2026-08-04 09:43:29 | 3702 | |||||
|
Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 | 2026-08-04 09:43:29 | 8838 | |||||||
|
RAST Server Resource Report Resource Website 500+ mentions |
RAST Server (RRID:SCR_014606) | RAST | production service resource, service resource | A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes. | microbiome, seed, annotate, genome, bacteria, archaea, service, bio.tools |
is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools |
National Science Foundation 0850546; NIAID contract HHSN272200900040C |
PMID:18261238 | Free for the scientific community, Login required | biotools:theseed | https://bio.tools/theseed | SCR_014606 | Rapid Annotation using Subsystem Technology, Rapid Annotation using Subsystem Technology Server | 2026-08-04 09:43:29 | 907 | ||||
|
SPEX2 Resource Report Resource Website 1+ mentions |
SPEX2 (RRID:SCR_014923) | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 | 2026-08-04 09:43:33 | 1 | ||||||||
|
libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | simulation software, software application, 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 | 2026-08-04 09:43:31 | 11 | ||||||
|
Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 | 2026-08-04 09:43:31 | 4876 | |||||||
|
MeroX Resource Report Resource Website 50+ mentions |
MeroX (RRID:SCR_014956) | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 | 2026-08-04 09:43:32 | 74 | |||||||
|
BUSCO Resource Report Resource Website 5000+ mentions |
BUSCO (RRID:SCR_015008) | data processing software, data analysis software, algorithm resource, software resource, software application | 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 |
Swiss National Science Foundation ; Marie Curie International Outgoing Fellowship |
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 | BUSCO v2, Benchmarking Universal Single-Copy Orthologs (BUSCO), Benchmarking Universal Single-Copy Orthologs, BUSCO v1 | 2026-08-04 09:43:33 | 7284 | |||||
|
DOGMA Resource Report Resource Website 100+ mentions |
DOGMA (RRID:SCR_015060) | web application, software resource | 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 | Dual Organellar GenoMe Annotator, Dual Organellar GenoMe Annotator (DOGMA) | 2026-08-04 09:43:35 | 413 | ||||||
|
GIIRA Resource Report Resource Website 1+ mentions |
GIIRA (RRID:SCR_015507) | data processing software, data analysis software, software resource, sequence analysis software, software application | Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment. | gene prediction, rna seq, coding region, potential coding region |
is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btt577 | Available for download | OMICS_07360 | http://www.rki.de/EN/Content/Institute/DepartmentsUnits/JuniorGroups/JRG4.html, https://sources.debian.org/src/giira/ | SCR_015507 | 2026-08-04 09:43:41 | 3 | |||||||
|
SeaView Resource Report Resource Website 1000+ mentions |
SeaView (RRID:SCR_015059) | data processing software, data analysis software, software resource, sequence analysis software, software application, data visualization software | 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 | 2026-08-04 09:43:33 | 1777 | |||||||
|
LTR_Finder Resource Report Resource Website 500+ mentions |
LTR_Finder (RRID:SCR_015247) | analysis service resource, web service, software resource, data access protocol, production service resource, service resource | 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 | LTR Finder | 2026-08-04 09:43:37 | 795 | |||||
|
SEER Resource Report Resource Website 100+ mentions |
SEER (RRID:SCR_015499) | data processing software, source code, data analysis software, software resource, sequence analysis software, software application | Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria. | bacterial genome association, sequence element enrichment analysis, kmer enrichment analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/ncomms12797 DOI:10.1101/038463 |
Available for download | OMICS_21699 | https://sources.debian.org/src/seer/ | SCR_015499 | 2026-08-04 09:43:41 | 463 | |||||||
|
primers4clades Resource Report Resource Website 1+ mentions |
primers4clades (RRID:SCR_015714) | web application, software resource | 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 | 2026-08-04 09:43:42 | 2 | ||||||
|
clustergrammer Resource Report Resource Website 10+ mentions |
clustergrammer (RRID:SCR_015681) | data visualization tool, software tool | Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features. | bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1038/sdata.2017.151 | biotools:clustergrammer | https://bio.tools/clustergrammer | SCR_015681 | 2026-08-04 09:43:43 | 41 | ||||||||
|
oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | data processing software, source code, data analysis software, software resource, software application | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | oligo package | 2026-08-04 09:43:42 | 1749 | |||||
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BSVF Resource Report Resource Website 1+ mentions |
BSVF (RRID:SCR_015727) | BSVF | data processing software, source code, data analysis software, software resource, sequence analysis software, software application | Software code for bisulfite sequencing virus integration. This finder is for directional libraries only and does not support PBAT and indirectional libraries. | virus integration, sequencing analysis, virus assembly, integration, bisulfite, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:bs-virus-finder | https://bio.tools/bs-virus-finder | SCR_015727 | BSVF: Bisulfite Sequencing Virus integration Finder, Bisulfite Sequencing Virus integration Finder | 2026-08-04 09:43:43 | 1 | ||||||
|
GenePattern Notebook Resource Report Resource Website 1+ mentions |
GenePattern Notebook (RRID:SCR_015699) | systems interoperability software, software resource, software application, web application, electronic laboratory notebook | Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. | gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools |
is listed by: bio.tools is listed by: Debian is affiliated with: GenePattern |
NIGMS R01-GM074024; NCI U24-CA194107 |
PMID:28822753 | Open Source, Free, Available for download, Account required | biotools:GenePattern_notebook | https://bio.tools/GenePattern_notebook | SCR_015699 | GenePattern Notebook environment | 2026-08-04 09:43:43 | 3 | |||||
|
DISEASES Resource Report Resource Website 500+ mentions |
DISEASES (RRID:SCR_015664) | database, data or information resource | Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence. | disease, gene, disease-gene association, text-mining, , bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation Center for Protein Research NNF14CC0001; European Union Seventh Framework Programme n259348 |
PMID:25484339 | biotools:diseases | https://bio.tools/diseases | SCR_015664 | 2026-08-04 09:43:43 | 627 | |||||||
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TISSUES Resource Report Resource Website 10+ mentions |
TISSUES (RRID:SCR_015665) | web application, software resource, database, data or information resource | Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. | tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools |
uses: BRENDA Tissue and Enzyme Source Ontology is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation NNF14CC0001; NCI U54 CA189205-01; CSIRO’s OCE Science Leader program |
PMID:26157623 | Freely available, Free, Available for download | biotools:tissues | https://bio.tools/tissues | SCR_015665 | TISSUES: Tissue Expression Database, Tissue Expression Database | 2026-08-04 09:43:42 | 42 |
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