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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | image analysis software, software application, data processing software, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-08-06 09:28:49 | 13 | ||||||
|
PASTEClassifier Resource Report Resource Website 10+ mentions |
PASTEClassifier (RRID:SCR_017645) | PASTEC | software application, data processing software, software resource | Software tool for automatic transposable element classification. Used for searching for structural features and similarity to classify transposable elements. | Automatic, transposable, element, classification, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
French National Research Agency | PMID:24786468 | Free, Available for download, Freely available | biotools:PAStEClassifier | https://urgi.versailles.inra.fr/download/repet/PASTEClassifier-1.0.tar.gz, https://bio.tools/repet, https://bio.tools/PASTEClassifier | SCR_017645 | Pseudo Agent System for Transposable Elements Classification, PASTEC | 2026-08-06 09:29:10 | 11 | ||||
|
Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software application, data processing software, software resource | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-08-06 09:29:07 | 59 | ||||||
|
MEGAHIT Resource Report Resource Website 1000+ mentions |
MEGAHIT (RRID:SCR_018551) | software application, data processing software, software resource | Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server. | NGS metagenome, Next Generation Sequencing assembler, metagenome, genome assembly, genome sequence, metagenomic dataset, giga base pairs, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Hong Kong GRF ; Innovation and Technology Fund |
PMID:25609793 PMID:27012178 |
Free, Available for download, Freely available | OMICS_07234, biotools:megahit | https://bio.tools/megahit, https://sources.debian.org/src/megahit/ | SCR_018551 | MEGAHIT v0.1 | 2026-08-06 09:29:27 | 1451 | |||||
|
TGS-GapCloser Resource Report Resource Website 10+ mentions |
TGS-GapCloser (RRID:SCR_017633) | software application, data processing software, software resource | Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes. | Error, prone, third, generation, sequencing, long, read, gap, closing, genome, assembly, contig, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:tGS-GapCloser | https://bio.tools/TGS-GapCloser | SCR_017633 | 2026-08-06 09:29:10 | 35 | ||||||||
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parSMURF Resource Report Resource Website 1+ mentions |
parSMURF (RRID:SCR_017560) | software application, data processing software, software resource | Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants. | High, performance, computing, imbalance, aware, machine, learning, genome, wide, detection, pathogenic, variant, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parsmurf | https://bio.tools/parsmurf | SCR_017560 | 2026-08-06 09:29:06 | 1 | ||||||||
|
EHRtemporalVariability Resource Report Resource Website 1+ mentions |
EHRtemporalVariability (RRID:SCR_018663) | software application, data processing software, software resource | Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users. | Delineating temporal data set shift, data set shift, electronic health record, temporal variability, delineate temporal data set shift, data dissimilarities, reliable data reuse, examine data set, biomedical data reuse, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Shiny |
DOI:10.1101/2020.04.07.20056564 | Free, Available for download, Freely available | biotools:ehrtemporalvariability | https://cran.r-project.org/web/packages/EHRtemporalVariability/readme/README.html, https://bio.tools/ehrtemporalvariability | SCR_018663 | Electronic Health Records temporal variability | 2026-08-06 09:29:28 | 3 | ||||||
|
rna-stability Resource Report Resource Website 1+ mentions |
rna-stability (RRID:SCR_019259) | software application, data processing software, software resource | Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species. | Secondary RNA structures generation, large scale generation, RNA structures, transcriptome folding statistics, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:rna-stability | https://bio.tools/rna-stability | SCR_019259 | 2026-08-06 09:29:27 | 1 | ||||||||
|
mosdepth Resource Report Resource Website 10+ mentions |
mosdepth (RRID:SCR_018929) | software application, data processing software, software resource | Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes. | Calculating genome, wide sequencing coverage, depth measurement, BAM file, CRAM file, nucleotide position, genome, genomic region set, WGS exom, targeted sequencing, coverage calculation, exom, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355; NCI U24 CA209999 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth, https://sources.debian.org/src/mosdepth/ | SCR_018929 | 2026-08-06 09:29:24 | 38 | ||||||
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RADAR-base Resource Report Resource Website 1+ mentions |
RADAR-base (RRID:SCR_019233) | portal, project portal, data or information resource | Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way. | Data collection, remote data collection, data collection platform, collecting mHealth datasets, mental health, mobile applications, remote sensing technology, telemedicine, bio.tools |
is listed by: bio.tools is listed by: Debian |
GSTT Charity ; Maudsley Charity ; NIHR Biomedical Research Centre at South London ; Maudsley NHS Foundation Trust ; King’s College London ; EU IMI2 ; UK National Institute for Health Research |
Free, Available for download, Freely available | biotools:RADAR-base | https://radar-base.org/index.php/getting-started-with-radar-base/, https://radar-base.org/index.php/getting-started-with-radar-base/demo-using-prmt-app/, https://bio.tools/RADAR-base | SCR_019233 | Remote Assessment of Disease And Relapses, Radar-base | 2026-08-06 09:29:32 | 1 | ||||||
|
Vienna RNA Resource Report Resource Website 100+ mentions |
Vienna RNA (RRID:SCR_008550) | database, data or information resource, software resource | This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Vienna; Vienna; Austria |
DOI:10.1186/1748-7188-6-26 | biotools:vienna_rna_package, nif-0000-31411, OMICS_09351 | https://bio.tools/vienna_rna_package, https://sources.debian.org/src/vienna-rna/ | SCR_008550 | Vienna RNA | 2026-08-06 09:27:10 | 404 | |||||||
|
Eukaryote Genes Resource Report Resource Website 10+ mentions |
Eukaryote Genes (RRID:SCR_008617) | database, data or information resource | Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information. | eukaryote, eukaryotic gene ontology, eukaryotic genome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Indiana University Center for Genomics and Bioinformatics ; NSF DBI 0090782; NSF DBI 9982851 |
Free, Freely available | nif-0000-31969, biotools:eugenes, SCR_013197, nif-0000-02818 | https://bio.tools/eugenes | SCR_008617 | euGenes | 2026-08-06 09:27:15 | 17 | ||||||
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GMAP Resource Report Resource Website 500+ mentions |
GMAP (RRID:SCR_008992) | GMAP | source code, software resource, image analysis software, alignment software, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing. | mrna, est sequence, expressed sequence tag, sequence, cdna sequence, genome, cdna, bio.tools |
is used by: deFuse is listed by: Debian is listed by: bio.tools has parent organization: Genentech |
PMID:15728110 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15072, biotools:gmap, nlx_152505 | https://bio.tools/gmap, https://sources.debian.org/src/gmap/ | SCR_008992 | 2026-08-06 09:27:15 | 594 | ||||||
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NetOGlyc Resource Report Resource Website 500+ mentions |
NetOGlyc (RRID:SCR_009026) | NetOGlyc | software resource, service resource, production service resource, data analysis service, software application, analysis service resource | Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins. | neural network, predict, mucin, galnac, o-glycosylation site, protein, o-glycosylation, glycoprotein, o-glycoproteome, glycosite, proteome, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CBS Prediction Servers |
PMID:23584533 | Acknowledgement requested | nlx_153864, biotools:netoglyc | https://bio.tools/netoglyc | SCR_009026 | NetOGlyc Server | 2026-08-06 09:27:19 | 601 | |||||
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elastix Resource Report Resource Website 100+ mentions |
elastix (RRID:SCR_009619) | elastix | software resource, image analysis software, registration software, software toolkit, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | reusable library, analyze, c++, console (text based), domain independent, nifti, nrrd, os independent, philips par/rec, registration, resampling, spatial transformation, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is related to: Insight Segmentation and Registration Toolkit has parent organization: Utrecht University; Utrecht; Netherlands |
PMID:19923044 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155845, biotools:elastix | http://www.nitrc.org/projects/elastix, https://bio.tools/elastix, https://sources.debian.org/src/elastix/ | SCR_009619 | 2026-08-06 09:27:21 | 167 | ||||||
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IMGT-ONTOLOGY Resource Report Resource Website |
IMGT-ONTOLOGY (RRID:SCR_010342) | IMGT-ONTOLOGY | controlled vocabulary, ontology, data or information resource | Ontology for immunogenetics and immunoinformatics. Provides semantic specification of terms to be used in immunogenetics and immunoinformatics and manages related knowledge, thus allowing standardization for immunogenetics data from genome, proteome, genetics, two-dimensional (2D) and three-dimensional (3D) structures. Manages the knowledge through diverse facets relying on seven axioms, IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, LOCALIZATION, ORIENTATION and OBTENTION. These axioms postulate that any object, any process and any relation can be identified, classified, described, numbered, localized and orientated, and the way it is obtained can be characterized. The axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. As the same axioms can be used to generate concepts for multi-scale level approaches, the Formal IMGT-ONTOLOGY represents a paradigm for system biology ontologies, which need to identify, to classify, to describe, to number, to localize and to orientate objects, processes and relations at the molecule, cell, tissue, organ, organism or population levels. IMGT, the international ImMunoGeneTics information system, has been built on IMGT-ONTOLOGY. The version 1.0.2 of IMGT-ONTOLOGY includes the concepts of IDENTIFICATION and the concepts of CLASSIFICATION. | owl, ontology, immunogenetics, immunoinformatics, terms semantic specification, bio.tools |
is listed by: BioPortal is listed by: Debian is listed by: bio.tools has parent organization: IMGT - the international ImMunoGeneTics information system |
Free, Freely available | nlx_157436, biotools:IMGt-ONtOLOGY | http://www.imgt.org/IMGTindex/ontology.php, https://bio.tools/IMGT-ONTOLOGY | SCR_010342 | 2026-08-06 09:27:32 | 0 | |||||||
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Evex Resource Report Resource Website 10+ mentions |
Evex (RRID:SCR_010509) | software resource, text-mining software, data or information resource, software application, database | EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature. | gene, protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium |
biotools:evex, nlx_158731 | https://bio.tools/evex | SCR_010509 | 2026-08-06 09:27:35 | 18 | |||||||||
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miRDB Resource Report Resource Website 1000+ mentions |
miRDB (RRID:SCR_010848) | miRDB | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | An online database for miRNA target prediction and functional annotations. | mirna, target, pathway, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18426918 PMID:18048393 |
OMICS_00403, biotools:miRDb | https://bio.tools/miRDB | SCR_010848 | 2026-08-06 09:27:40 | 1862 | |||||||
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Glimmer Resource Report Resource Website 500+ mentions |
Glimmer (RRID:SCR_011931) | Glimmer | software resource, service resource, production service resource, data analysis service, analysis service resource | A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. | microbial, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Glimmer-MG is related to: GlimmerHMM has parent organization: Johns Hopkins University; Maryland; USA |
DOI:10.1093/nar/26.2.544 | Open unspecified license, OSI certified | OMICS_01486, biotools:glimmer | https://bio.tools/glimmer, https://sources.debian.org/src/tigr-glimmer/ | SCR_011931 | Glimmer - Microbial Gene-Finding System | 2026-08-06 09:27:48 | 637 | |||||
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MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | software resource, alignment software, image analysis software, software toolkit, data processing software, software application | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ | SCR_011811 | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-08-06 09:27:50 | 22450 |
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