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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PROMALS3D Resource Report Resource Website 50+ mentions |
PROMALS3D (RRID:SCR_018161) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints. | Structure alignment, 3D structure, sequence, protein, amino acid, homolog identification | DOI:10.1093/nar/gkn072 | Free, Freely available | SCR_018161 | 2026-08-29 11:25:59 | 50 | ||||||||||
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SnapTools Resource Report Resource Website 10+ mentions |
SnapTools (RRID:SCR_018097) | SnapTools | alignment software, data processing software, image analysis software, software application, software resource | Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets. | Sequence, snap file, single nucleus, ATACseq dataset, data | is used by: scATAC Pipeline | Free, Available for download, Freely available | SCR_018097 | Single Nucleus Accessibility Profile Tools, Single nucleus accessibility profile Tools | 2026-08-29 11:25:57 | 16 | ||||||||
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EMBL-EBI COVID-19 Portal Resource Report Resource Website 10+ mentions |
EMBL-EBI COVID-19 Portal (RRID:SCR_018337) | data or information resource, data repository, database, disease-related portal, portal, service resource, storage service resource, topical portal | EMBL-EBI portal to enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets submitted to EMBL-EBI and other major centers for biomedical data. Used to facilitate data sharing and analysis to accelerate coronavirus research. The aim of the COVID-19 Data Portal is to facilitate data sharing and analysis, and to accelerate coronavirus research. EMBL-EBI and partners have set up the COVID-19 Data Portal, which will bring together relevant datasets submitted to EMBL-EBI and other major centres for biomedical data. The aim is to facilitate data sharing and analysis, and to accelerate coronavirus research. The COVID-19 Data Portal will enable researchers to upload, access and analyse COVID-19 related reference data and specialist datasets. The COVID-19 Data Portal will be the primary entry point into the functions of a wider project, the European COVID-19 Data Platform. | COVID-19, COVID-19 data, sequence, expression, protein sequence, protein structure, proteome, translatome, analysis, EMBL-EBI | is related to: EMBL-EBI Pathogens - COVID-19 | COVID-19 | Free, Freely available | SCR_018816 | https://www.covid19dataportal.org/, https://www.ebi.ac.uk/about/news/press-releases/embl-ebi-launches-covid-19-data-portal | SCR_018337 | EMBL-EBI COVID-19 Data Portal, COVID-19 Data Portal | 2026-08-29 11:26:06 | 20 | ||||||
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2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation Resource Report Resource Website 1+ mentions |
2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) | 2019nCoVR | data or information resource, disease-related portal, portal, topical portal | Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data. | COVID-19, sequence, genome sequence, genome variation, data, China National Center for Bioinformation | COVID-19 | Free, Freely available | SCR_018342 | 2019 Novel Coronavirus Resource, 2019 Novel Coronavirus Resource (2019nCoVR), CNCB 2019nCoVR, CNCB 2019 Novel Coronavirus Resource | 2026-08-29 11:26:06 | 4 | ||||||||
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GeMoMa Resource Report Resource Website 100+ mentions |
GeMoMa (RRID:SCR_017646) | simulation software, software application, software resource | Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species. | Homology, based, gene, prediction, model, target, evolutionary, related, reference, species, sequence, conservation, intron, position, RNAseq, data, protein, coding, transcript, bio.tools |
is listed by: bio.tools is listed by: Debian works with: GUSHR |
PMID:31020559 | Free, Available for download, Freely available | biotools:gemoma | https://bio.tools/gemoma | SCR_017646 | Gene Model Mapper | 2026-08-29 11:27:42 | 158 | ||||||
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
NCI R01 CA120185; NCI R01 CA134292; NHGRI R01 HG006102; NHGRI R01 HG006677; NIGMS R01 GM105705; the Cancer Prevention and Research Institute of Texas |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | 2026-08-29 11:27:40 | 4976 | ||||||
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PseudoFuN Resource Report Resource Website 1+ mentions |
PseudoFuN (RRID:SCR_017095) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families. | gene, pseudogene, sequence, homology, regulatory, network, miRNA, coexpression, noncoding, RNA, TCGA, cancer |
has parent organization: Ohio State University; Ohio; USA has parent organization: Indiana University School of Medicine; Indiana; USA |
NLM T15 LM011270 | Free, Freely available | https://github.com/yanzhanglab/PseudoFuN_app | SCR_017095 | Pseudogene Functional Networks | 2026-08-29 11:27:42 | 2 | |||||||
|
Hinge Resource Report Resource Website 1+ mentions |
Hinge (RRID:SCR_016135) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution. | long, read, genome, assembly, hinging, sequence, optimal, repeat, resolution |
is listed by: Debian is listed by: OMICtools |
PMID:28320918 | Free, Available for download | OMICS_12339 | https://sources.debian.org/src/hinge/ | SCR_016135 | 2026-08-29 11:28:07 | 9 | |||||||
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SMARTdenovo Resource Report Resource Website 100+ mentions |
SMARTdenovo (RRID:SCR_017622) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as de novo assembler for PacBio and Oxford Nanopore data. It produces assembly from all-vs-all raw read alignments without error correction stage. Allows to read overlapping, rescue missing overlaps, identify low-quality regions and chimaera and produce better consensus. | De novo, assembler, PacBio, Oxford Nanopore, data, sequence, raw, read, alignment, error, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:SMARTdenovo, biotools:SMARtdenovo | https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo, https://bio.tools/SMARTdenovo | SCR_017622 | 2026-08-29 11:27:45 | 191 | ||||||||
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duphold Resource Report Resource Website 1+ mentions |
duphold (RRID:SCR_016938) | data analysis software, data processing software, software application, software resource | Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data. | annotate, structural, variation, call, sequence, depth, confidence, predict, copy, number, short, long, read, data | is listed by: OMICtools | Free, Available for download, Freely available | SCR_016938 | 2026-08-29 11:27:41 | 3 | ||||||||||
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FreeContact Resource Report Resource Website 10+ mentions |
FreeContact (RRID:SCR_016113) | alignment software, data processing software, image analysis software, software application, software resource | Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud). | protein, structure, prediction, sequence, analysis, fast, contact, alignment, multiple |
is listed by: OMICtools is related to: Debian |
Alexander von Humboldt Foundation ; German Ministry for Research and Education (BMBF: Bundesministerium fuer Bildung und Forschung) ; Research Council of Norway 208481 |
PMID:24669753 DOI:10.1186/1471-2105-15-85 |
Open source, Free, Available for download | OMICS_03520 | https://rostlab.org/owiki/index.php/FreeContact, https://sources.debian.org/src/libfreecontact-perl/ | SCR_016113 | 2026-08-29 11:28:07 | 22 | ||||||
|
QModeling Resource Report Resource Website 1+ mentions |
QModeling (RRID:SCR_016358) | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences. | statistical, parametric, mapping, reference, region, kinetic, model, dynamic, analysis, brain, data, imaging, sequence |
is related to: University of Malaga; Andalusia; Spain is related to: MATLAB |
DOI:10.1007/s12021-018-9384-y | Free, Available for download, Available after registration | SCR_016358 | 2026-08-29 11:27:41 | 1 | |||||||||
|
OGDraw Resource Report Resource Website 100+ mentions |
OGDraw (RRID:SCR_017337) | OGDRAW | data processing software, data visualization software, service resource, software application, software resource, software toolkit | Software package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers. | graphical, visualization, organellar, genome, convert, annotation, GenBank, format, map, DNA, sequence | works with: GenBank | Max Planck Society | PMID:30949694 | Free, Freely available | SCR_017337 | Draw Organelle Genome Maps, OrganellarGenomeDRAW | 2026-08-29 11:27:44 | 359 | ||||||
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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 | NanoPipe, nanopipe2 | 2026-08-29 11:27:43 | 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 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-08-29 11:28:10 | 2 | ||||
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ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882; Wellcome Trust WT082930MA |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-08-29 11:28:06 | 8 | ||||||
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TMHMM Server Resource Report Resource Website 1000+ mentions |
TMHMM Server (RRID:SCR_014935) | software resource, web application | Web application for the prediction of transmembrane helices in proteins using Hidden Markov Models. FASTA formatted sequences can be uploaded via file or copy-paste, and output can be formatted as extensive with graphics, extensive without graphics, or one line per protein. Submissions are limited to 10,000 sequences and 4,000,000 amino acids - each sequence is limited to no more than 8,000 amino acids. | sequence, amino acid, web application, transmembrane helices, hidden markov model, fasta | Open source | SCR_014935 | TMHMM Server v 2.0 | 2026-08-29 11:27:54 | 2154 | ||||||||||
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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 | 2026-08-29 11:28:24 | 39 | |||||||
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Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | 2026-08-29 11:26:16 | 56 | ||||||||
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Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-08-29 11:25:07 | 83 |
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