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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pilon Resource Report Resource Website 1000+ mentions |
Pilon (RRID:SCR_014731) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome. | automatically, improve, draft, assembly, variation, strain, genome, read, alignment, analysis, inconsistency, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: shovill is hosted by: GitHub |
DOI:10.1371/journal.pone.0112963 DOI:10.1371/journal.pone.0112963 |
Available for download, Acknowledgement requested | OMICS_14553, biotools:pilon | https://github.com/broadinstitute/pilon/wiki, https://bio.tools/pilon, https://sources.debian.org/src/pilon/ | SCR_014731 | SciCrunch Registry | 2026-09-26 02:17:12 | 3377 | |||||||
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RepeatModeler Resource Report Resource Website 1000+ mentions |
RepeatModeler (RRID:SCR_015027) | data analysis software, data processing software, sequence analysis software, software application, software resource | Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis, sequence repeats, repeat identification, bio.tools |
uses: RepeatScout is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Dfam |
Institute for Systems Biology ; NHGRI R44 HG02244; NHGRI R01 HG002939 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:repeatmodeler | https://bio.tools/repeatmodeler | SCR_015027 | SciCrunch Registry | 2026-09-26 02:17:13 | 3249 | |||||||
|
Morpheus Resource Report Resource Website 500+ mentions |
Morpheus (RRID:SCR_014975) | 3d visualization software, data processing software, data visualization software, simulation software, software application, software resource | Modeling and simulation environment for study of multi scale and multicellular systems. Users can construct and simulate models of gene regulation, signaling pathways, tissue patterning and morphogenesis and explore the effects of multiscale feedbacks between these processes. Morpheus can render 2D and 3D models using graphical user interface. | simulation, modeling, multicellular, systems biology, cell-based models, data visualization, differential equations, reaction-diffusion systems, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Dresden University of Technology; Saxony; Germany |
BMBF 0315734; BMBF 0316169; DFG |
PMID:24443380 | Free, Available for download, Freely available | biotools:morpheus-framework | https://gitlab.com/morpheus.lab/morpheus, https://bio.tools/morpheus-framework | https://imc.zih.tu-dresden.de/wiki/morpheus | SCR_014975 | SciCrunch Registry | 2026-09-26 02:17:16 | 754 | |||||
|
MEBS: Multigenomic Entropy-Based Score Resource Report Resource Website 1+ mentions |
MEBS: Multigenomic Entropy-Based Score (RRID:SCR_015708) | MEBS | data analysis software, data processing software, software application, software resource | Open source software to evaluate, quantify, compare, and predict the metabolic machinery of interest in large ‘omic’ datasets. This protocol finds informative protein families and uses them to score metagenomic sets. | metagenomics analysis, metabolism, fasta file, protein analysis, omic dataset, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source, Available for download | biotools:mebs | https://bio.tools/mebs | SCR_015708 | SciCrunch Registry | metagenome_Pfam_score, Multigenomic Entropy-Based Score, Multigenomic Entropy-Based Score (MEBS) | 2026-09-26 02:17:13 | 1 | ||||||
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Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/, https://bio.tools/g2d | SCR_008190 | SciCrunch Registry | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-09-26 02:17:10 | 2 | |||||
|
FragGeneScan Resource Report Resource Website 100+ mentions |
FragGeneScan (RRID:SCR_011929) | data analysis software, data processing software, sequence analysis software, software application, software resource | A software application for finding fragmented genes in short reads and may be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. | microbiome, sequence analysis, fragment, gene, short read, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Acknowledgement requested, Available for download | OMICS_01484, biotools:fraggenescan | http://omics.informatics.indiana.edu/FragGeneScan/, https://bio.tools/fraggenescan | SCR_011929 | SciCrunch Registry | 2026-09-26 02:17:11 | 190 | ||||||||
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RNA FRABASE - RNA FRAgments search engine and dataBASE Resource Report Resource Website |
RNA FRABASE - RNA FRAgments search engine and dataBASE (RRID:SCR_012808) | RNA FRABASE | analysis service resource, d spatial image, data analysis service, data or information resource, database, production service resource, service resource | Engine and database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation. The database contains RNA sequences and secondary structures, described in the dot-bracket notation, derived from PDB-deposited RNA structures and their complexes. It also contains atom coordinates of the unmodified and modified nucleotide and nucleoside residues extracted from the PDB-deposited RNA structures, as well as torsion and pseudotorsion angle values, sugar pucker parameters and classification of base pair types given for the PBD-deposited RNA structures. Knowledge of the three dimensional RNA structure is crucial for all fields of biomolecular research. In contrast to the protein field, only about 1.300 experimentally derived structures of RNAs are deposited in the Protein Data Bank (PDB). To complement the results of experimental studies, new approaches based on bioinformatics and calculation are pursued in several laboratories to make tertiary RNA structure prediction possible. RNA FRABASE version 2.0 should greatly facilitate various RNA structure modelling approaches, RNA structure analysis and motif searching. If one compares the three dimensional RNA structure to a spatial puzzle, the RNA FRABASE allows to pull out a defined piece of this puzzle - the 3D RNA fragment. The architecture of the web-accessible RNA FRABASE engine and database is based on the following information path: PDB-deposited RNA structures �� RNA sequences and secondary structures described in the dot-bracket notation �� secondary structures of RNA fragments �� 3D RNA fragments. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide on the spot structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. | structural element, secondary structure, rna, rna structure, 3d rna fragment, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Polish Academy of Sciences Poznan; Poznan; Poland |
Foundation for Polish Science SP 01/04; Ministry of Education and Science 3T09A014 29; Polish Ministry of Science and Higher Education PBZ-MniSW-07/1/2007/01; Polish Ministry of Science and Higher Education NN 519314635 |
PMID:20459631 PMID:17921499 |
nif-0000-03413, biotools:rna_frabase | https://bio.tools/rna_frabase | SCR_012808 | SciCrunch Registry | RNA FRAgments search engine dataBASE, RNA FRAgments search engine and dataBASE, RNA FRABASE - RNA FRAgments search engine dataBASE | 2026-09-26 02:17:11 | 0 | |||||
|
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 | SciCrunch Registry | Gene Model Mapper | 2026-09-26 02:17:15 | 158 | ||||||
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Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. | Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools works with: Scoary |
Wellcome Trust | PMID:26198102 | Free, Available for download, Freely available | OMICS_09491, biotools:roary | https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ | SCR_018172 | SciCrunch Registry | 2026-09-26 02:17:18 | 710 | ||||||
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R/qtl2 Resource Report Resource Website 10+ mentions |
R/qtl2 (RRID:SCR_018181) | data analysis software, data processing software, software application, software resource | Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. | High density genotyping data, molecular phenotype, gene expression, proteomics, mapping trait loci, diversity outbred mice, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM070683; NIGMS R01 GM074244; NIGMS R01 GM123489 |
PMID:30591514 | Free, Available for download, Freely available | biotools:R_qtl2, SCR_020965 | https://bio.tools/R_qtl2, https://kbroman.org/qtl2, https://github.com/rqtl/qtl2 | SCR_018181 | SciCrunch Registry | QTL, R/quantitative trait loci, QTL2, Quantitative Trait Locus 2, quantitative trait loci 2, R/qtl, qtl2 | 2026-09-26 02:17:16 | 13 | |||||
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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 | SciCrunch Registry | 2026-09-26 02:17:14 | 4976 | ||||||
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CMap Resource Report Resource Website 500+ mentions |
CMap (RRID:SCR_016204) | data or information resource, data set, database, software resource, web application | Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines. | data, set, connectivity, gene, expression, database, heat map, drug, tool, perturbational, perturbagen, signature, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Free for academic use, Subscription for commercial use, Available for download, Acknowledgement requested | biotools:CMap | https://bio.tools/CMap | SCR_016204 | SciCrunch Registry | LINCS CMap L1000, LINCS L1000, LINCS CMap, ConnectivityMap, Connectivity Map | 2026-09-26 02:17:14 | 789 | |||||||
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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 | SciCrunch Registry | 2026-09-26 02:17:17 | 191 | ||||||||
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pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | data acquisition software, data processing software, image acquisition software, software application, software resource, software toolkit | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap, https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf, https://bio.tools/pheatmap, https://sources.debian.org/src/r-cran-pheatmap/ | SCR_016418 | SciCrunch Registry | pretty heatmap | 2026-09-26 02:17:17 | 1249 | ||||||
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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 | 2026-09-26 02:17:16 | 1 | ||||||
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HH-suite Resource Report Resource Website 50+ mentions |
HH-suite (RRID:SCR_016133) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments. | protein, sensitive sequence search, pairwise alignment, multiple database, homologous structure, prediction, modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
Excellence Initiative of the Bundesministerium für Bildung und Forschung ; Ludwig-Maximilians Universität Munich ; the Deutsche Forschungsgemeinschaft grant SFB646 |
DOI:10.1186/s12859-019-3019-7 | Free, Available for download, Freely available | biotools:hh-suite | https://bio.tools/hh-suite | http://toolkit.genzentrum.lmu.de/sections/search | SCR_016133 | SciCrunch Registry | 2026-09-26 02:17:14 | 53 | |||||
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JAMM Resource Report Resource Website 1+ mentions |
JAMM (RRID:SCR_017049) | data analysis software, data processing software, software application, software resource | Software tool as peak finder for joint analysis of NGS replicates. Used for peak finding in next generation sequencing broad and narrow datasets like ChIP-Seq, ATAC-Seq, DNase-Seq. Can integrate information from biological replicates and assign peak boundaries accurately. | peak, finder, sequencing, dataset, integrate, replicate, boundary, accurately, bio.tools |
is listed by: Debian is listed by: bio.tools |
Max-Delbrück-Center/New York University Exchange Program. | PMID:25223640 | Free, Available for download, Freely available | biotools:jamm | https://bio.tools/jamm | SCR_017049 | SciCrunch Registry | J oint A nalysis of NGS replicates via M ixture M odel clustering, Joint Analysis of NGS replicates via Mixture Model clustering | 2026-09-26 02:17:17 | 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 | 2026-09-26 02:17:18 | 37 | ||||||
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NetPhos Resource Report Resource Website 100+ mentions |
NetPhos (RRID:SCR_017975) | analysis service resource, data access protocol, production service resource, service resource, software application, software resource, standalone software, web service | Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package. | Neural network, predict, phosphorylation site, independent sequence, protein, kinase, serine, threonine, tyrosine, eukaryotic, bio.tools |
is used by: YinOYang is listed by: Debian is listed by: bio.tools has parent organization: Technical University of Denmark; Lyngby; Denmark |
PMID:10600390 | Free, Freely available | biotools:netphos | https://bio.tools/netphos | http://www.cbs.dtu.dk/services/NetPhos-2.0/ | SCR_017975 | SciCrunch Registry | NetPhos 3.1, NetPhos 2.0 | 2026-09-26 02:17:15 | 448 | |||||
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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 | 2026-09-26 02:17:14 | 5 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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