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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CYANA Resource Report Resource Website 100+ mentions |
CYANA (RRID:SCR_014229) | data processing software, software application, data analysis software, software resource | Software for automated structure calculation of biological macromolecules on basis of conformational constraints from nuclear magnetic resonance. Program for automated NMR protein structure calculation. CYANA requires a sufficient list of assigned chemical shifts and lists of cross-peak positions and columns from 2D, 3D, or4D NOESY spectra in order to calculate the assignment of the NOESY cross-peaks and the 3D structure of the protein in solution. | protein structure, nmr, noesy, 3d structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Goethe University Frankfurt am Main; Hessen; Germany has parent organization: RIKEN |
PMID:15318003 PMID:25801209 |
Available to the academic community, Available to commercial user, Pay for license | SCR_021949, biotools:cyana | http://www.las.jp/english/products/cyana.html, https://bio.tools/cyana, https://dbpedia.org/page/CYANA_(software) | SCR_014229 | 2026-07-30 09:29:13 | 425 | |||||||
|
SCRATCH Resource Report Resource Website 100+ mentions |
SCRATCH (RRID:SCR_014291) | service resource, data access protocol, software resource, web service, production service resource, analysis service resource | Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server. | Protein predictor, secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts, tertiary structure prediction, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:15980571 | Free, Freely available | biotools:scratch | https://bio.tools/scratch | http://www.igb.uci.edu/servers/psss.html | SCR_014291 | Scratch Protein Predictor | 2026-07-30 09:29:07 | 136 | |||||
|
CentroidFold Resource Report Resource Website 10+ mentions |
CentroidFold (RRID:SCR_017253) | data access protocol, simulation software, software resource, web service, software application | Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator. | RNA, secondary, structure, prediction, centroid, estimator, sequecne, data, alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
New Energy and Industrial Technology Development Organization of Japan ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; Internal fund of Computational Biology Research Center |
PMID:19435882 | Free, Freely available | biotools:centroidfold, OMICS_03449 | https://bio.tools/centroidfold | SCR_017253 | 2026-07-30 09:30:18 | 15 | ||||||
|
ape Resource Report Resource Website 10+ mentions |
ape (RRID:SCR_017343) | data processing software, software application, data analysis software, software resource | Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R. | analysis, phylogenetics, evolution, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: CRAN |
PMID:30016406 PMID:14734327 PMID:22495750 |
Free, Available for download, Freely available | biotools:ape | https://cran.r-project.org/web/packages/ape/ape.pdf, http://ape-package.ird.fr/, https://bio.tools/ape | SCR_017343 | ape 3.0, ape 5.0, Analysis of Phylogenetics and Evolution | 2026-07-30 09:30:19 | 42 | ||||||
|
prank Resource Report Resource Website 100+ mentions |
prank (RRID:SCR_017228) | data processing software, software toolkit, software resource, alignment software, image analysis software, software application | Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences. | multiple, nucleotide, sequence, alignment, DNA, codon, amino acid, phylogenetic, gap, predict, location, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:24170401 PMID:21110866 |
Free, Available for download, Freely available | biotools:prank, SCR_024174, OMICS_12425 | https://www.ebi.ac.uk/goldman-srv/webprank/, https://ariloytynoja.github.io/prank-msa/, https://bio.tools/prank | https://omictools.com/prank-tool | SCR_017228 | PRANK | 2026-07-30 09:30:17 | 253 | |||||
|
SeQuiLa Resource Report Resource Website 1+ mentions |
SeQuiLa (RRID:SCR_017220) | data processing software, software application, data analysis software, software resource | Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals. | genomic, intervals, querying, processing, Apache, Spark, SQL, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Warsaw University of Technology; Warsaw; Poland |
National Science Center ; Polish budget funds for science |
PMID:30428005 | Free, Available for download, Freely available | biotools:SeQuiLa-cov | http://biodatageeks.org/sequila/, https://bio.tools/SeQuiLa-cov | SCR_017220 | 2026-07-30 09:30:07 | 1 | ||||||
|
VETA Resource Report Resource Website 1+ mentions |
VETA (RRID:SCR_017201) | data processing software, data analysis software, data visualization software, software resource, software application, data acquisition software | Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS. | Electromyography, transcranial, magnetic, stimulation, analysis, EMG, TMS, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCATS TR002370 | PMID:31572120 | Free, Available for download, Freely available | BioTools:VETA, biotools:VEtA | https://github.com/greenhouselab/Veta/tree/master/data, https://bio.tools/VETA, https://bio.tools/VETA, https://bio.tools/VETA | SCR_017201 | 2026-07-30 09:30:17 | 2 | ||||||
|
GraphClust2 Resource Report Resource Website 1+ mentions |
GraphClust2 (RRID:SCR_017286) | data processing software, web application, data analysis software, software resource, software application | Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function. | scalable, clustering, RNA, sequence, secondary, structure, function, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
German Research Foundation Collaborative Research Centre 992 Medical Epigenetics ; German Federal Ministry of Education and Research |
PMID:31808801 PMID:22689765 |
Free, Available for download, Freely available | biotools:GraphClust2 | https://bio.tools/GraphClust2 | SCR_017286 | GraphClust, GraphClust-2 | 2026-07-30 09:30:18 | 4 | |||||
|
Proovread Resource Report Resource Website 10+ mentions |
Proovread (RRID:SCR_017331) | data processing software, sequence analysis software, data analysis software, software resource, software application | Software tool for PacBio hybrid error correction through iterative short read consensus. | PacBio, hybrid, error, correction, short, read, consensus, DNA, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BWA is related to: BLASR is related to: SHRiMP |
European Research Council | PMID:25015988 | Free, Available for download, Freely available | biotools:proovread | https://bio.tools/proovread | SCR_017331 | 2026-07-30 09:30:19 | 12 | ||||||
|
PatchDock Resource Report Resource Website 50+ mentions |
PatchDock (RRID:SCR_017589) | data access protocol, simulation software, software resource, web service, software application | Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles. | Molecular, docking, structure, prediction, protein, molecule, shape, complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Israel Science Foundation ; Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University ; Israeli Ministry of Science ; National Cancer Institute ; NIH |
PMID:15980490 | Free, Freely available | biotools:patchdock | https://bio.tools/patchdock | SCR_017589 | 2026-07-30 09:30:22 | 85 | ||||||
|
miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | data access protocol, software resource, web service, data or information resource, database | Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. | Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Saarland University ; Germany |
PMID:27742822 | biotools:miRPathDb | https://bio.tools/miRPathDB | SCR_017356 | miRNA Pathway Dictionary Database | 2026-07-30 09:30:13 | 52 | ||||||
|
refgenie Resource Report Resource Website 1+ mentions |
refgenie (RRID:SCR_017574) | software application, software resource, data management software, service resource | Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis. | Organize, retrive, share, genome, analysis, reference, assembly, asset, manager, sequence, annotation, file, command, line, interface, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/698704 | Free, Available for download, Freely available | biotools:Refgenie | https://bio.tools/Refgenie | SCR_017574 | reference genome manager | 2026-07-30 09:30:11 | 6 | ||||||
|
European Variation Archive (EVA) Resource Report Resource Website 50+ mentions |
European Variation Archive (EVA) (RRID:SCR_017425) | EVA | service resource, data repository, data or information resource, database, storage service resource | Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser. | Collection, genetic, variation, data, chromosomal, location, dbSNP, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:eva | https://bio.tools/eva | SCR_017425 | EVA, European Variation Archive | 2026-07-30 09:30:10 | 89 | ||||||
|
Galaxy scater Resource Report Resource Website 1+ mentions |
Galaxy scater (RRID:SCR_017394) | data processing software, sequence analysis software, service resource, software toolkit, data analysis software, training service resource, source code, software resource, software application | Software tool as Galaxy based training resource for single cell RNA-seq quality control and analyses. | scRNA-seq, single, cell, scater, Galaxy, training, quality, control, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC BBS/E/T/000PR9817; BBSRC BBS/E/T/000PR9818; BBSRC BBS/E/T/000PR9819; BBSRC CCG:BBS/E/T/000PR9816 |
DOI:10.1101/724047 | Free, Available for download, Freely available | biotools:Galaxy_scater | https://bio.tools/Galaxy_scater | SCR_017394 | 2026-07-30 09:30:09 | 1 | ||||||
|
fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | data processing software, software application, data analysis software, software resource | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-07-30 09:30:19 | 23 | |||||||
|
ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | service resource, data access protocol, software resource, web service, production service resource, analysis service resource | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-07-30 09:30:31 | 2 | |||||||
|
SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | software resource, web application | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/, https://bio.tools/SnpHub | SCR_018177 | 2026-07-30 09:30:19 | 1 | |||||||
|
SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | data processing software, software application, data analysis software, software resource | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; Wellcome Trust ; European Research Council |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-07-30 09:30:26 | 2 | ||||||
|
Multiple Myeloma survival predictor Resource Report Resource Website 1+ mentions |
Multiple Myeloma survival predictor (RRID:SCR_017651) | data access protocol, web service, software resource, service resource | Dockerized environment for winning algorithm in 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3. | Multiple Myeloma, prognostic model, survival analysis, GuanRank, bio.tools |
is listed by: bio.tools is listed by: Debian |
Multiple Myeloma | Restricted | biotools:Multiple_Myeloma_survival_prediction | https://bio.tools/Multiple_Myeloma_survival_prediction | SCR_017651 | 2026-07-30 09:30:23 | 2 | |||||||
|
MCScan Resource Report Resource Website 10+ mentions |
MCScan (RRID:SCR_017650) | data processing software, sequence analysis software, software toolkit, data analysis software, software resource, software application | Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format. | Simultaneously, scan, multiple, genome, identify, homologous, chromosomal, region, align, gene, anchor, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Georgia; Georgia; USA |
Free, Available for downoad, Freely available | biotools:MCScan | http://chibba.agtec.uga.edu/duplication/mcscan/, https://bio.tools/MCScan | SCR_017650 | Multiple Collinearity Scan | 2026-07-30 09:30:12 | 37 |
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