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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) | 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 | ||||||
|
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 | |||||||
|
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 | |||||
|
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 | |||||||
|
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 | |||||
|
HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | data processing software, source code, data analysis software, software resource, sequence analysis software, software application | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2, https://bio.tools/hisat2, https://sources.debian.org/src/hisat2/ | SCR_015530 | HISAT | 2026-08-04 09:43:41 | 17595 | |||||
|
Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | data processing software, data analysis software, software resource, software application, data visualization software, software toolkit | Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Engineering Research Development Center W912HZ-11-P-0019; NSF DMR-1005413 |
PMID:22889332 DOI:10.1186/1758-2946-4-17 |
Open source, Free, Free to download | OMICS_04967, biotools:avogadro | http://avogadro.openmolecules.net/, https://github.com/avogadro, https://bio.tools/avogadro, https://sources.debian.org/src/axe-demultiplexer/ | SCR_015983 | 2026-08-04 09:43:46 | 1965 | ||||||
|
Hybrid-denovo Resource Report Resource Website 1+ mentions |
Hybrid-denovo (RRID:SCR_015866) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software for a de novo OTU-picking pipeline integrating single- and paired-end 16S sequence tags. It is designed to take Illumina paired-end sequencing reads as input and output the OTU BIOM table, together with their representative sequences and a phylogenetic tree of OTUs. | hybrid-denovo, 16S rRNA, microbiota pipeline, single-end, paired-end, illumina read, de novo, otu-picking pipeline, phylogenetic tree, python, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:hybrid-denovo | https://bio.tools/hybrid-denovo | SCR_015866 | 2026-08-04 09:43:45 | 3 | |||||||||
|
Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT098051; Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ | SCR_015993 | 2026-08-04 09:43:46 | 51 | |||||
|
NiftyPET Resource Report Resource Website 1+ mentions |
NiftyPET (RRID:SCR_015873) | data processing software, source code, software resource, software application, image analysis software, data visualization software, software toolkit | Python software package that offers quantitative PET image reconstruction and analysis with high accuracy and precision. It is written in CUDA C and embedded in Python C extensions. | python, cuda c, python c, pet, image reconstruction, image analysis, bio.tools |
uses: CMake is listed by: Debian is listed by: bio.tools |
DOI:10.1007/s12021-017-9352-y | Free, Available for download, Runs on Windows, Runs on Linux | biotools:niftypet | https://bio.tools/niftypet | SCR_015873 | 2026-08-04 09:43:44 | 6 | |||||||
|
andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | data processing software, alignment software, algorithm resource, software resource, software application, image analysis software | 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 | 2026-08-04 09:43:46 | 41 | ||||||
|
SeqBuster Resource Report Resource Website 10+ mentions |
SeqBuster (RRID:SCR_009616) | data processing software, software application, software resource, data analysis software | Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells. | small RNAs datasets, ubiquitous miRNA modifications, human embryonic cells, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Spanish Ministry of Health ; CIBERESP ; Sixth Framework Programme of the European Commission ; Spanish Ministry of Science and Innovation |
PMID:20008100 | Free, Available for download, Freely available | OMICS_00367, biotools:seqbuster | https://bio.tools/seqbuster | SCR_009616 | 2026-08-04 09:42:25 | 30 | ||||||
|
GMA Resource Report Resource Website |
GMA (RRID:SCR_009212) | GMA | data processing software, data analysis software, time-series analysis software, software resource, software application | Software package to perform Granger mediation analysis for time series. Includes single level GMA model and two-level GMA model, for time series with hierarchically nested structure. | Granger, meditation, analysis, time, series, level, GMA, model, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
NIBIB EB022911 | PMID:31070732 | Free, Available for download, Freely available | nlx_154361, biotools:GMA | https://github.com/chaoning/GMA, https://bio.tools/GMA | http://www.montana.edu/kalinowski/GMA/GMA_Home.htm | SCR_009212 | Granger Mediation Analysis | 2026-08-04 09:42:19 | 0 | |||
|
BeeBase Resource Report Resource Website 50+ mentions |
BeeBase (RRID:SCR_008966) | BeeBase | data analysis service, analysis service resource, data set, production service resource, service resource, database, data or information resource | Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.BeeBase is an archive and will not be updated. The most up-to-date bee genome data is now available through the navigation bar on the HGD Home page. | genome, gene set, sequence, bee, genomics, entomology, blast, annotation, pest, pathogen, honey, beehive, insect, bee pollen, bee product, bee culture, pollination, pollinator, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: University of Missouri; Missouri; USA |
Texas Agricultural Experiment Station ; Golden Heritage Foods and Sioux Honey Association ; NHGRI 5-P41-HG000739-13; USDA 2008-35302-18804 |
PMID:21071397 | Open unspecified license, Acknowledgement requested, Data Usage Policy | nlx_152034, biotools:hgd, r3d100010925 | https://bio.tools/hgd, https://doi.org/10.17616/R3Z629 | SCR_008966 | Hymenoptera Genome Database | 2026-08-04 09:42:16 | 56 | ||||
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R/QTLBIM Resource Report Resource Website 1+ mentions |
R/QTLBIM (RRID:SCR_009375) | software application, software toolkit, software resource, software library | Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154597, biotools:qtlbim | http://www.ssg.uab.edu/qtlbim/index.jsp, https://cran.r-project.org/src/contrib/Archive/qtlbim/, https://bio.tools/qtlbim | http://www.qtlbim.org/ | SCR_009375 | 2026-08-04 09:42:22 | 2 | ||||||||
|
MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data processing software, software application, software resource, data analysis software | QTL analysis based on imputed dosages/posterior_probabilities. | genetic association, genomic analysis, imaging genomics, snp, gene, quantitative trait analysis, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 DOI:10.1002/gepi.20533 |
Free, Non-commercial, Acknowledgement requested | nlx_155856, biotools:mach | http://www.nitrc.org/projects/mach, https://bio.tools/mach | https://sources.debian.org/src/mach-haplotyper/ | SCR_009621 | mach2qtl, MaCH | 2026-08-04 09:42:26 | 925 |
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