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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NanoPipe Resource Report Resource Website 1+ mentions |
NanoPipe (RRID:SCR_016852) | NanoPipe | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms. | analysis, MinION, long, sequence, read, Oxford Nanopore, alignment, target, statistics, polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Muenster; Muenster; Germany |
Institute of Bioinformatics Muenster ; Germany |
PMID:30689855 | Free, Available for download, Freely Available | biotools:NanoPipe | https://github.com/IOB-Muenster/nanopipe2, https://bio.tools/NanoPipe | SCR_016852 | SciCrunch Registry | NanoPipe, nanopipe2 | 2026-09-19 12:55:16 | 5 | ||||
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DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | SciCrunch Registry | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-09-19 12:55:16 | 2 | ||||
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REDIportal Resource Report Resource Website 10+ mentions |
REDIportal (RRID:SCR_018490) | atlas, data or information resource, database, portal, service resource, topical portal | Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms. Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided. | A-to-I RNA Editing Events, RNA editing events collection, atlas, database, GTEx project, genomic region, gene name, RNAseq, DNAseq, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CLAIRE is related to: SIGNOR |
Consiglio Nazionale delle Ricerche ; Italian Ministero dell Istruzione |
PMID:27587585 | Free, Freely available | biotools:rediportal | https://bio.tools/rediportal | SCR_018490 | SciCrunch Registry | 2026-09-19 12:55:18 | 37 | ||||||
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MB-GAN Resource Report Resource Website 1+ mentions |
MB-GAN (RRID:SCR_019289) | simulation software, software application, software resource | Software tool as deep learning simulation framework for simulating realistic microbiome data. Can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from it. | Metagenomics, deep learning, generative adversarial network, microbiome data simulation, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Texas at Dallas; Texas; USA |
DOI:10.1101/863977 | Free, Available for download, Freely available | biotools:mb-gan | https://bio.tools/mb-gan | SCR_019289 | SciCrunch Registry | Microbiome Simulation via Generative Adversarial Network | 2026-09-19 12:55:18 | 1 | ||||||
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iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | SciCrunch Registry | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-09-19 12:55:28 | 0 | ||||||
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Composition Profiler Resource Report Resource Website 10+ mentions |
Composition Profiler (RRID:SCR_014630) | software resource, web application | Web tool for discovery and visualization of differences in amino acid composition. Two samples of amino acid sequences serve as input and a bar chart composed of twenty data points is output. | web tool, web application, amino acid, amino acid composition, sequence, bar chart, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17578581 | Source code available, Acknowledgement requested | biotools:composition_profiler | https://bio.tools/composition_profiler | SCR_014630 | SciCrunch Registry | 2026-09-19 12:55:29 | 39 | |||||||
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CAZy- Carbohydrate Active Enzyme Resource Report Resource Website 1000+ mentions |
CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) | CAZy | data or information resource, database | Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site. | carbohydrate, carbohydrate-binding, carbohydrate binding module, carbohydrate esterase, catalytic binding, glycosidic bond, glycosidic hydrolase, glycosyl transferase, polysaccharide lyase, enzyme class, enzyme, module, genome, virus, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Aix-Marseille University; Provence-Alpes-Cote d'Azur; France |
PMID:24270786 | r3d100012321, biotools:cazy, OMICS_01677, nif-0000-02642, SCR_012935 | https://bio.tools/cazy | SCR_012909 | SciCrunch Registry | Carbohydrate-Active enZYme, Carbohydrate-Active enZYmes Database | 2026-09-19 12:55:31 | 2435 | ||||||
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ProP Server Resource Report Resource Website 50+ mentions |
ProP Server (RRID:SCR_014936) | software resource, web application | Web application which predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase prediction. | web application, prediction, arginine, lysine, cleavage, propeptide, eukaryotic, protein, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/protein/gzh013 | Open source | biotools:prop, BioTools:prop | https://bio.tools/prop, https://bio.tools/prop, https://bio.tools/prop | SCR_014936 | SciCrunch Registry | ProP, ProP 1.0 Server, ProP 1.0 | 2026-09-19 12:55:31 | 78 | ||||||
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GeneWise Resource Report Resource Website 1000+ mentions |
GeneWise (RRID:SCR_015054) | software resource, web application | Gene alignment tool from the EBI which predicts gene structure using similar protein sequences. See also the associated GenomeWise tool. | gene alignment, dna sequence, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:15123596 | Freely available, Available for download | biotools:wise | https://bio.tools/wise | SCR_015054 | SciCrunch Registry | 2026-09-19 12:55:31 | 1079 | |||||||
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mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | data processing software, software application, software resource | Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | SciCrunch Registry | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-09-19 12:55:49 | 0 | ||||||
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SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | data processing software, software application, software resource | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SciCrunch Registry | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-09-19 12:55:49 | 403 | |||||
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iDASH Resource Report Resource Website 1+ mentions |
iDASH (RRID:SCR_003524) | iDASH | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications. | data sharing, computing, biomedical, behavior, molecular, phenotyping, kawasaki disease, hematologic medication, individualized intervention, physical activity, phenotype, data set, image, cyberinfrastructure, schema, domain model, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: DataCite is related to: National Centers for Biomedical Computing is related to: NIH Data Sharing Repositories is related to: National Centers for Biomedical Computing has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIH Roadmap for Bioinformatics and Computational Biology ; NHLBI U54 HL108460 |
PMID:22081224 | THIS RESOURCE IS NO LONGER IN SERVICE | https://api.datacite.org/dois?prefix=10.15147, biotools:iDASH, nif-0000-38239 | https://bio.tools/iDASH | SCR_003524 | SciCrunch Registry | iDASH Repository, Integrating Data for Analysis Anonymization and SHaring | 2026-09-19 12:55:52 | 2 | ||||
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biobambam Resource Report Resource Website 50+ mentions |
biobambam (RRID:SCR_003308) | data processing software, software application, software resource | Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1751-0473-9-13 | Free, Available for download, Freely available | biotools:biobambam, OMICS_04664 | https://bio.tools/biobambam, https://sources.debian.org/src/biobambam2/ | SCR_003308 | SciCrunch Registry | 2026-09-19 12:55:52 | 65 | |||||||
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Phenoscape Resource Report Resource Website 10+ mentions |
Phenoscape (RRID:SCR_003799) | Phenoscape | data or information resource, portal | Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions. | phenotype, bio.tools |
is listed by: Debian is listed by: bio.tools is parent organization of: Teleost Anatomy Ontology is parent organization of: Vertebrate Taxonomy Ontology is parent organization of: Phenoscape Knowledgebase |
NSF DBI-1062404; NSF DBI-1062542; NSF BDI-0641025; NSF EF-0905606; NSF EF-0423641 |
biotools:Phenoscape, nlx_158096 | https://bio.tools/Phenoscape | SCR_003799 | SciCrunch Registry | 2026-09-19 12:55:52 | 10 | |||||||
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FASTX-Toolkit Resource Report Resource Website 1000+ mentions |
FASTX-Toolkit (RRID:SCR_005534) | data processing software, software application, software resource, software toolkit | Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. | Short reads, FASTA file, FASTQ file, preprocessing, command line tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
SCR_019035, SCR_015042, biotools:fastx-toolkit, OMICS_01045 | https://github.com/agordon/fastx_toolkit, https://bio.tools/fastx-toolkit | SCR_005534 | SciCrunch Registry | FASTQ/A short-reads pre-processing tools | 2026-09-19 12:55:55 | 2864 | ||||||||
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Mammalian Gene Collection Resource Report Resource Website 10+ mentions |
Mammalian Gene Collection (RRID:SCR_007024) | MGC | biomaterial supply resource, cell repository, material resource | NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cell line, cdna, frozen, clone, vector, gene, open reading frame, sequence, expressed sequence tag, bio.tools, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: ATCC is related to: GenBank is related to: Invitrogen Clones is related to: Open Biosystems is related to: Zebrafish Gene Collection has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | biotools:mammalian_gene_collection, nif-0000-00195 | https://bio.tools/mammalian_gene_collection | SCR_007024 | SciCrunch Registry | Mammalian Gene Collection | 2026-09-19 12:55:56 | 46 | |||||
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Sickle Resource Report Resource Website 1000+ mentions |
Sickle (RRID:SCR_006800) | Sickle | data processing software, software application, software resource | Software tool for windowed adaptive trimming for fastq files using quality. Supports quality values like Illumina, Solexa, and Sanger. Takes the quality values and slides a window across them whose length is 0.1 times the length of the read. | bio.tools, windowed, adaptive, trimming, FASTQ, quality, value, read |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | OMICS_01077, biotools:sickle, SCR_016901 | https://bio.tools/sickle, https://sources.debian.org/src/sickle/ | SCR_006800 | SciCrunch Registry | sickle - A windowed adaptive trimming tool for FASTQ files using quality | 2026-09-19 12:55:56 | 1664 | ||||||
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SeqTrace Resource Report Resource Website 50+ mentions |
SeqTrace (RRID:SCR_005580) | SeqTrace | data processing software, software application, software resource | A software application for viewing and processing DNA sequencing chromatograms (trace files) that makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. SeqTrace also includes a full-featured trace file viewer and editor. You can view your sequencing chromatograms at a variety of scales and zoom levels, simultaneously view matching forward and reverse traces, edit the called bases, and export individual DNA sequences as well as forward/reverse alignments. SeqTrace supports popular trace file formats, including ABIF, SCF, and ZTR. | dna sequencing trace file, dna sequencing, trace file, trace, python, gtk, chromatogram, graphic, sequence analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code has parent organization: University of Colorado Boulder; Colorado; USA |
PMID:22942788 | GNU General Public License, v3 | OMICS_01021, biotools:seqtrace | https://bio.tools/seqtrace | SCR_005580 | SciCrunch Registry | Seqtrace - User-friendly software for viewing and processing DNA sequencing trace files | 2026-09-19 12:55:55 | 64 | |||||
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RESCUE-ESE Resource Report Resource Website 50+ mentions |
RESCUE-ESE (RRID:SCR_008496) | data or information resource, database, organization portal, portal | Specific short oligonucleotide sequences that enhance pre-mRNA splicing when present in exons, termed exonic splicing enhancers (ESEs), play important roles in constitutive and alternative splicing (ESE References). A hybrid computational/experimental method, RESCUE-ESE, was recently developed for identifying sequences with ESE activity. In this approach, specific hexanucleotide sequences are identified as candidate ESEs on the basis that they have both significantly higher frequency of occurrence in exons than in introns and also significantly higher frequency in exons with weak (non-consensus) splice sites than in exons with strong (consensus) splice sites. Representative hexamers from ten different classes of candidate ESEs, together with 6 or 7 bases of flanking sequence context on each side, were introduced into a weak (poorly spliced) exon in a splicing reporter construct. These reporter minigenes were then transfected into cultured cells, where they are transcribed and spliced, and the relative level of inclusion of the test exon was assayed by quantitative (radio-labeled) RT-PCR. Point mutants of these sequences were also analyzed to confirm the precise motifs responsible for ESE activity. The RESCUE-ESE approach identified 238 hexamers as candidate ESEs using a large database of human genes of known exon-intron structure containing over 30,000 nonredudant exons. In more recent analyses by Yeo et al., the RESCUE-ESE approach was utilized to predict hexamers as candidate ESEs in other vertebrate genes, namely, Fugu rubipes, Zebrafish and Mouse. This allows the identification of motifs that are conserved in vertebrates. This web server allows a sequence to be checked for presence of these candidate ESE hexamers. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
biotools:rescue-ese, nif-0000-31403 | https://bio.tools/rescue-ese | http://genes.mit.edu/burgelab/rescue-ese/ | SCR_008496 | SciCrunch Registry | RESCUE-ESE | 2026-09-19 12:55:58 | 96 | |||||||
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HCLUST Resource Report Resource Website 1000+ mentions |
HCLUST (RRID:SCR_009154) | HCLUST | software application, software resource | Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:h-clust, SCR_009102, nlx_154195, nlx_154331 | https://bio.tools/h-clust | SCR_009154 | SciCrunch Registry | R/HCLUST | 2026-09-19 12:55:59 | 1460 |
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