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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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) | 2026-10-31 12:16:25 | 428 | ||||||
|
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) | 2026-10-31 12:16:19 | 17 | |||||
|
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 | 2026-10-31 12:16:29 | 1817 | |||||||
|
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 | 2026-10-31 12:16:19 | 74 | |||||||
|
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 | 2026-10-31 12:16:27 | 8320 | |||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | 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 | SciCrunch Registry | 2026-10-31 12:16:40 | 33 | ||||||
|
Centrifuge Classifier Resource Report Resource Website 10+ mentions |
Centrifuge Classifier (RRID:SCR_016665) | data analysis software, data processing software, sequence analysis software, software application, 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 |
NHGRI R01 HG006677; NIGMS R01 GM083873; NSF ABI1356078; U. S. Army Research Office W911NF1410490 |
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 | SciCrunch Registry | 2026-10-31 12:16:40 | 10 | ||||||
|
TB PORTALS Resource Report Resource Website 10+ mentions |
TB PORTALS (RRID:SCR_016594) | consortium, data or information resource, data repository, disease-related portal, organization portal, portal, service resource, storage service resource, topical portal | 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 | SciCrunch Registry | 2026-10-31 12:16:39 | 20 | |||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | data processing software, data visualization software, software application, software resource | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow, https://bio.tools/nmrprocflow, https://github.com/inra/nmrprocflow | SCR_016592 | SciCrunch Registry | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-10-31 12:16:50 | 29 | |||||
|
CheckM Resource Report Resource Website 100+ mentions |
CheckM (RRID:SCR_016646) | data analysis software, data processing software, software application, software resource, software toolkit | Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. | assess, quality, microbial, genome, recovered, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/gr.186072.114 | Free, Available for download, Freely available | biotools:checkm | https://github.com/Ecogenomics/CheckM, https://bio.tools/checkm | SCR_016646 | SciCrunch Registry | 2026-10-31 12:16:51 | 238 | |||||||
|
Genotyping Resource Report Resource Website 10+ mentions |
Genotyping (RRID:SCR_016645) | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Web tool to identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus. | identify, genotype, viral, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | biotools:ncbi_genotyping | https://bio.tools/ncbi_genotyping | SCR_016645 | SciCrunch Registry | 2026-10-31 12:16:45 | 40 | ||||||||
|
Libra Resource Report Resource Website |
Libra (RRID:SCR_016608) | data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource | 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 | SciCrunch Registry | 2026-10-31 12:16:39 | 0 | |||||||
|
KAT Resource Report Resource Website 10+ mentions |
KAT (RRID:SCR_016741) | KAT | data analysis software, data processing software, software application, software resource, software toolkit | Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies. | generate, analyse, compare, k-mer, spectra, sequence, file, quality, control, NGS, dataset, genome, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC | DOI:10.1093/bioinformatics/btw663 | Free, Available for download, Freely available | biotools:kat | http://www.earlham.ac.uk/kat-tools, https://bio.tools/kat | SCR_016741 | SciCrunch Registry | K-mer Analysis Toolkit | 2026-10-31 12:16:53 | 21 | ||||
|
CCTOP Resource Report Resource Website 10+ mentions |
CCTOP (RRID:SCR_016963) | CCTOP | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web application providing transmembrane topology prediction. Server incorporates topology information from existing experimental and computational sources using the probabilistic framework of hidden Markov model. Provides the option to precede the topology prediction with signal peptide prediction and transmembrane globular protein discrimination. Given the amino acid sequence of a putative α helical transmembrane protein, CCTOP predicts its topology i.e. localization of membrane spanning regions and orientation of segments between them. | transmembrane, topology, prediction, signal, peptide, globular, protein, discrimination, amino, acid, sequence, region, orientation, segment, bio.tools |
is listed by: Debian is listed by: bio.tools works with: PDBTM works with: Topology Data Bank of Transmembrane Proteins works with: TopDom |
Hungarian Scientific Research Fund | PMID:25943549 | Free, Freely available | biotools:cctop | https://bio.tools/cctop | SCR_016963 | SciCrunch Registry | CCTOP, Consensus Constrained TOPology | 2026-10-31 12:16:55 | 31 | ||||
|
Illuminating the Druggable Genome Resource Report Resource Website 50+ mentions |
Illuminating the Druggable Genome (RRID:SCR_016924) | IDG | consortium, data or information resource, data repository, organization portal, portal, service resource, storage service resource | Program to improve understanding of properties and functions of proteins that are currently unannotated within three most commonly drug protein families: targeted G-protein coupled receptors, ion channels, and protein kinases. Includes Data and Resource Generating Centers (DRGC), Knowledge Management Center (KMC), and Resource Dissemination and Outreach Center (RDOC). | understudied, target, protein, G protein, coupled, receptor, ion, channel, kinase, bio.tools |
is recommended by: National Library of Medicine is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian |
NIH Common Fund | biotools:pharos | https://pharos.nih.gov/, https://bio.tools/pharos, https://darkmatter.ucsf.edu/about | https://druggablegenome.net | SCR_016924 | SciCrunch Registry | Pharos, Illuminating the Druggable Genome, IDG, Illuminating Druggable Genome | 2026-10-31 12:16:43 | 64 | |||||
|
Thunder STORM Resource Report Resource Website 10+ mentions |
Thunder STORM (RRID:SCR_016897) | ThunderSTORM | data analysis software, data processing software, software application, software resource, software toolkit | Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging. | automated, processing, analysis, visualization, data, acquired, single, molecule, localization, microscopy, SMLM, imaging, bio.tools |
is listed by: Debian is listed by: bio.tools is a plug in for: ImageJ |
Charles University ; Czech Science Foundation ; European Regional Development Fund ; European Social Fund |
PMID:24771516 | Free, Available for download, Freely available | biotools:thunderstorm | https://bio.tools/thunderstorm | SCR_016897 | SciCrunch Registry | 2026-10-31 12:16:46 | 48 | |||||
|
CRISPR-P Resource Report Resource Website 10+ mentions |
CRISPR-P (RRID:SCR_016941) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment. | synthetic, single, RNA, CRISP, plant, Cas9, target, DNA, sequence, analysis, restriction, enzyme, sgRNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Fundamental Research Funds for the Central Universities ; National Basic Research Program of China ; Program for New Century Excellent Talents in University |
PMID:24719468 | Free, Freely available | biotools:CRISPR-P | https://bio.tools/CRISPR-P | SCR_016941 | SciCrunch Registry | CRISPR-P 2.0, Clustered Regularly Interspaced Short Palindromic Repeats P, CRISPR P | 2026-10-31 12:16:43 | 42 | |||||
|
ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data analysis software, data processing software, software application, software resource | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat, https://www.crick.ac.uk/research/labs/peter-van-loo/software, https://bio.tools/ascat, https://sources.debian.org/src/r-other-ascat/ | SCR_016868 | SciCrunch Registry | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-10-31 12:16:42 | 42 | |||||
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EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, image processing software, software application, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | SciCrunch Registry | EMAN1, EMAN2 | 2026-10-31 12:16:42 | 107 | |||
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clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. | data, statistical, analysis, visualization, gene, cluster, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
2007 Chang-Jiang Scholars Program ; Fundamental Research Funds for the Central Universities ; Guangdong Natural Science Research Grant ; National 973 Projects of China ; National Natural Science Foundation of China |
PMID:22455463 | Free, Available for download, Freely available | biotools:clusterprofiler | https://github.com/GuangchuangYu/clusterProfiler, https://guangchuangyu.github.io/software/clusterProfiler/, https://bio.tools/clusterprofiler | SCR_016884 | SciCrunch Registry | Cluster Profiler | 2026-10-31 12:16:43 | 13465 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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