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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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larvalign Resource Report Resource Website 1+ mentions |
larvalign (RRID:SCR_015815) | data analysis software, data or information resource, data processing software, data set, sequence analysis software, software application, software resource, software toolkit | Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping. | drosophila melanogaster, computational method, gene expression, alignment, larval brain, larvae, template generation, mapping, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download | biotools:larvalign | https://bio.tools/larvalign | SCR_015815 | 2026-09-12 12:58:31 | 1 | ||||||||
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Canu Resource Report Resource Website 1000+ mentions |
Canu (RRID:SCR_015880) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). | long-read, assembly, k-mer, weighting, repeat separation, adaptive, pacbio, single-molecule, sequencing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is related to: Celera assembler |
National Human Genome Research Institute ; National Science Foundation NSF IOS-1237993; US Department of Homeland Security (DHS) HSHQDC-07-C-00020 |
PMID:28298431 DOI:10.1101/071282 |
Free, Available for download | OMICS_14592, biotools:canu | http://canu.readthedocs.io/en/latest/, https://bio.tools/canu, https://sources.debian.org/src/canu/ | SCR_015880 | 2026-09-12 12:58:32 | 2451 | ||||||
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Genesis Resource Report Resource Website 1000+ mentions |
Genesis (RRID:SCR_015775) | data analysis software, data processing software, data visualization software, software application, software resource | Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments. | cluster analysis, microarray data, java, gene expression, visualization, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:11836235 | Free for academic use, Free for non-profits, Available for download, Runs on Windows, Runs on Mac OS, Runs on Linux | biotools:genesis_microarray | https://bio.tools/genesis_microarray | SCR_015775 | Genesis: Cluster analysis of microarray data | 2026-09-12 12:58:30 | 1029 | ||||||
|
Avogadro Resource Report Resource Website 1000+ mentions |
Avogadro (RRID:SCR_015983) | data analysis software, data processing software, data visualization software, software application, software resource, 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 | 2026-09-12 12:58:33 | 2237 | ||||||
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Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | data analysis software, data processing software, sequence analysis software, software application, software resource, 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 |
Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1; Wellcome Trust WT098051 |
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 | 2026-09-12 12:58:33 | 56 | |||||
|
Barrnap Resource Report Resource Website 500+ mentions |
Barrnap (RRID:SCR_015995) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:barrnap, OMICS_13988 | https://github.com/tseemann/barrnap, https://bio.tools/barrnap, https://sources.debian.org/src/barrnap/ | SCR_015995 | Barrnap: Basic rapid ribosomal RNA predictor | 2026-09-12 12:58:33 | 722 | |||||||
|
andi Resource Report Resource Website 10+ mentions |
andi (RRID:SCR_015971) | algorithm resource, alignment software, data processing software, image analysis software, software application, software resource | 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 | 2026-09-12 12:58:33 | 41 | ||||||
|
DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 |
Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology ; EU NoE BIOPATTERN contract no. FP6-508803; EU STREP APrIL II contract no. FP6-508861 |
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 | 2026-09-12 12:58:34 | 71 | ||||
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TopFIND Resource Report Resource Website 10+ mentions |
TopFIND (RRID:SCR_008918) | TopFIND | data or information resource, data repository, database, service resource, storage service resource | An integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases. It lists more than 120,000 N- and C-termini and almost 10,000 cleavages. TopFIND is a resource for comprehensive coverage of protein N- and C-termini discovered by all available in silico, in vitro as well as in vivo methodologies. It makes use of existing knowledge by seamless integration of data from UniProt and MEROPS and provides access to new data from community submission and manual literature curating. It renders modifications of protein termini, such as acetylation and citrulination, easily accessible and searchable and provides the means to identify and analyse extend and distribution of terminal modifications across a protein. The data is presented to the user with a strong emphasis on the relation to curated background information and underlying evidence that led to the observation of a terminus, its modification or proteolytic cleavage. In brief the protein information, its domain structure, protein termini, terminus modifications and proteolytic processing of and by other proteins is listed. All information is accompanied by metadata like its original source, method of identification, confidence measurement or related publication. A positional cross correlation evaluation matches termini and cleavage sites with protein features (such as amino acid variants) and domains to highlight potential effects and dependencies in a unique way. Also, a network view of all proteins showing their functional dependency as protease, substrate or protease inhibitor tied in with protein interactions is provided for the easy evaluation of network wide effects. A powerful yet user friendly filtering mechanism allows the presented data to be filtered based on parameters like methodology used, in vivo relevance, confidence or data source (e.g. limited to a single laboratory or publication). This provides means to assess physiological relevant data and to deduce functional information and hypotheses relevant to the bench scientist. TopFIND PROVIDES: * Integration of protein termini with proteolytic processing and protein features * Displays proteases and substrates within their protease web including detailed evidence information * Fully supports the Human Proteome Project through search by chromosome location CONTRIBUTE * Submit your N- or C-termini datasets * Contribute information on protein cleavages * Provide detailed experimental description, sample information and raw data | protein, n-termini, c-termini, protease, protein cleavage, proteomics, cleavage site, terminus, modification, proteolytic processing, protein function, domain structure, protein termini, terminus modification, protease, substrate, protease inhibitor, protein interaction, protein-protein interaction, interaction, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: UniProtKB is related to: PSICQUIC Registry is related to: MEROPS has parent organization: University of British Columbia; British Columbia; Canada |
Canadian Institutes of Health Research ; Cancer Research Society ; British Columbia Proteomics Network ; Metalloproteinase Proteomics and Systems Biology ; Michael Smith Foundation for Health Research ; Breast Cancer Society of Canada ; Alexander von Humboldt-Stiftung ; BMBF ; German Academic Exchange Service |
PMID:22102574 PMID:21822272 |
Public, Acknowledgement requested | biotools:topfind, r3d100012721, nlx_151607 | https://bio.tools/topfind, https://doi.org/10.17616/R3KB8J, https://doi.org/10.17616/R3KB8J | SCR_008918 | Termini oriented protein Function Inferred Database | 2026-09-12 12:57:10 | 29 | ||||
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FGDP Resource Report Resource Website |
FGDP (RRID:SCR_008910) | FGDP | software resource | A Java-based, Microarray or Genechip data analysis system. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Fox Chase Cancer Center |
PMID:14734324 | GNU General Public License | OMICS_00756, biotools:fgdp | https://bio.tools/fgdp | SCR_008910 | Functional Genomics Data Pipeline (FGDP), Functional Genomics Data Pipeline | 2026-09-12 12:57:10 | 0 | |||||
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Generic GO Term Finder Resource Report Resource Website 100+ mentions |
Generic GO Term Finder (RRID:SCR_008870) | GOTermFinder, GO-TermFinder, GO Term Finder, GO::TermFinder | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource, source code | The Generic GO Term Finder finds the significant GO terms shared among a list of genes from an organism, displaying the results in a table and as a graph (showing the terms and their ancestry). The user may optionally provide background information or a custom gene association file or filter evidence codes. This tool is capable of batch processing multiple queries at once. GO::TermFinder comprises a set of object-oriented Perl modules GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. This implementation, developed at the Lewis-Sigler Institute at Princeton, depends on the GO-TermFinder software written by Gavin Sherlock and Shuai Weng at Stanford University and the GO:View module written by Shuai Weng. It is made publicly available through the GMOD project. The full source code and documentation for GO:TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, graph, visualization, genomics, gene association, ontology or annotation visualization, term enrichment, ontology, process, function, component, enrichment, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Generic Model Organism Database Project has parent organization: Princeton University; New Jersey; USA has parent organization: Comprehensive Perl Archive Network |
NHGRI 1R01HG002732 | PMID:15297299 | Free for academic use | nlx_149293, biotools_go_term_finder | https://bio.tools/go_term_finder | SCR_008870 | Generic Gene Ontology (GO) Term Finder, Generic Gene Ontology Term Finder | 2026-09-12 12:57:10 | 108 | ||||
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LegumeIP Resource Report Resource Website 10+ mentions |
LegumeIP (RRID:SCR_008906) | LegumeIP | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression. | gene function, genome evolution, legume, gene, genome, plant, genomics, transcriptomic, gene annotation, gene family, synteny, gene expression, blast, genomic sequence, microarray, rna-seq, comparative genomics, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: UniProt is related to: InterProScan is related to: Gene Ontology is related to: KEGG has parent organization: Samuel Roberts Noble Foundation |
Samuel Roberts Noble Foundation ; NSF ABI-0960897 |
PMID:22110036 | biotools:legumeip, nlx_151455 | https://bio.tools/legumeip | SCR_008906 | LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes, LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes | 2026-09-12 12:57:10 | 23 | |||||
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GMA Resource Report Resource Website |
GMA (RRID:SCR_009212) | GMA | data analysis software, data processing software, software application, software resource, time-series analysis software | 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 | 2026-09-12 12:57:11 | 0 | |||
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BeeBase Resource Report Resource Website 50+ mentions |
BeeBase (RRID:SCR_008966) | BeeBase | analysis service resource, data analysis service, data or information resource, data set, database, production service resource, service 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 | 2026-09-12 12:57:11 | 56 | ||||
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R/QTLBIM Resource Report Resource Website 1+ mentions |
R/QTLBIM (RRID:SCR_009375) | software application, software library, software resource, software toolkit | 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 | 2026-09-12 12:57:12 | 2 | ||||||||
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iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-09-12 12:57:12 | 11 | ||||||
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SeqBuster Resource Report Resource Website 10+ mentions |
SeqBuster (RRID:SCR_009616) | data analysis software, data processing software, software application, software resource | 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 |
CIBERESP ; Sixth Framework Programme of the European Commission ; Spanish Ministry of Health ; Spanish Ministry of Science and Innovation |
PMID:20008100 | Free, Available for download, Freely available | OMICS_00367, biotools:seqbuster | https://bio.tools/seqbuster | SCR_009616 | 2026-09-12 12:57:14 | 31 | ||||||
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MACH Resource Report Resource Website 500+ mentions |
MACH (RRID:SCR_009621) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:57:14 | 937 | |||||
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SpliceMap Resource Report Resource Website 10+ mentions |
SpliceMap (RRID:SCR_009650) | SpliceMap | software resource | A de novo splice junction discovery and alignment tool. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:25577377 PMID:20371516 |
OMICS_01252, biotools:splicemap | https://bio.tools/splicemap | SCR_009650 | 2026-09-12 12:57:14 | 21 | |||||||
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IsoEM Resource Report Resource Website 10+ mentions |
IsoEM (RRID:SCR_009993) | IsoEM | software resource | Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Connecticut; Connecticut; USA |
biotools:isoem, OMICS_01278 | https://bio.tools/isoem | SCR_009993 | 2026-09-12 12:57:15 | 10 |
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