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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PrognoScan Resource Report Resource Website 100+ mentions |
PrognoScan (RRID:SCR_018740) | service resource, production service resource, data or information resource, analysis service resource, database | Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets. | Kyushu Institute of Technology, meta analysis, prognostic gene value, cancer microarray dataset, clinical annotation, gene expression, tumor marker, therapeutic target, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:19393097 | Free, Freely available | SCR_018741, biotools:prognoscan | http://dna00.bio.kyutech.ac.jp/PrognoScan/index.html, https://bio.tools/prognoscan | SCR_018740 | 2026-08-06 09:29:29 | 366 | |||||||
|
Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs. | Coevolutionary sequence analysis, evolutionary coupling, protein sequence, RNA sequence alignment, predict protein structure, evolutionary sequence covariantion, 3D protein structure prediction, , bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF GRFP DGE1144152; DOE CSGF fellowship ; NIGMS R01 GM106303 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | EVcouplings | 2026-08-06 09:29:21 | 24 | |||||
|
CRISPR-ERA Resource Report Resource Website 10+ mentions |
CRISPR-ERA (RRID:SCR_018710) | service resource, data access protocol, web service, software resource | Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design. | Design tool, CRISPR mediated gene editing, gene repression, gene activation, guide RNA design, genome, automated genome, sgRNA design, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
NIH Office of The Director ; NIDCR ; NSFC ; FANEDD ; NIH Office of the Director OD017887; NIDA R01 DA036858 |
PMID:26209430 | Free, Freely available | biotools:CRISPR-ERA | https://bio.tools/CRISPR-ERA | SCR_018710 | CRISP-Editing, Repression and Activation | 2026-08-06 09:29:21 | 10 | |||||
|
GalaxyWEB Resource Report Resource Website 100+ mentions |
GalaxyWEB (RRID:SCR_018558) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined. | Protein structure prediction, protein structure refinement, protein sequence, template based modeling, model structure, loop location, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
National Research Foundation of Korea ; Ministry of Land ; Transport and Maritime Affairs of Korea ; Seoul National University |
PMID:22649060 | Free, Freely available | biotools:galaxyweb | https://bio.tools/galaxyweb | SCR_018558 | 2026-08-06 09:29:20 | 157 | ||||||
|
MaxAlign Resource Report Resource Website 10+ mentions |
MaxAlign (RRID:SCR_018552) | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area. | Maximizing data, post process alignment, gap free column alignment area, sequence subset selection, improve alignment area, bio.tools |
is listed by: Debian is listed by: bio.tools |
Foundation for Science and Technology Portuguese Ministry of Science. | PMID:17725821 | Free, Available for download, Freely available | biotools:maxalign | https://bio.tools/maxalign | SCR_018552 | MaxAlign 1.1, MaxAlign 1.1 Server | 2026-08-06 09:29:20 | 11 | |||||
|
MiXCR Resource Report Resource Website 50+ mentions |
MiXCR (RRID:SCR_018725) | data analysis software, software application, software resource, data processing software | Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling. | Process immunome data, raw sequence, quantitated clonotype, B cell receptor, sequencing data analysis, T cell receptor, high throughput sequencing data, adaptive immunity profiling, MiLaboratory, bio.tools |
is listed by: Debian is listed by: bio.tools |
Russian Science Foundation | PMID:25924071 | Restricted | biotools:MiXCR, BioTools:MiXCR | https://github.com/milaboratory/mixcr, https://bio.tools/MiXCR, https://bio.tools/MiXCR, https://bio.tools/MiXCR | SCR_018725 | 2026-08-06 09:29:29 | 59 | ||||||
|
HPEPDOCK Server Resource Report Resource Website 10+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; Huazhong University of Science and Technology |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-08-06 09:29:20 | 46 | ||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | software toolkit, data access protocol, web service, software resource | Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models. | Molecular structure description, molecular complex, atom, bond, protein, complex, modification, crosslinked residue, semantic meaning description, bio.tools |
is used by: BpForms is used by: ObjTables is listed by: Debian is listed by: bio.tools is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bcforms | https://bio.tools/bcforms | SCR_018654 | 2026-08-06 09:29:21 | 0 | ||||||
|
GalaxyRefine Resource Report Resource Website 100+ mentions |
GalaxyRefine (RRID:SCR_018531) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. | Protein structure prediction, protein, structure prediction, protein structure, molecular dynamics simulation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
National Research Foundation of Korea ; Seoul National University. |
PMID:23737448 | biotools:galaxyrefine | https://bio.tools/galaxyrefine | SCR_018531 | 2026-08-06 09:29:20 | 248 | |||||||
|
EpiEstim Resource Report Resource Website 10+ mentions |
EpiEstim (RRID:SCR_018538) | software resource, data analysis software, software toolkit, data processing software, software application | Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series. | Estimate time varying, reproduction number, epidemics, quantify transmissibility, time series analysis, reproductionc number analysis, incidence time series, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
United Kingdom Medical Research Council | PMID:24043437 | Free, Available for download, Freely available | biotools:EpiEstim | https://bio.tools/EpiEstim | SCR_018538 | Estimate Time Varying Reproduction Numbers from Epidemic Curves | 2026-08-06 09:29:20 | 32 | |||||
|
precrec Resource Report Resource Website 1+ mentions |
precrec (RRID:SCR_018659) | software application, data analytics software, software toolkit, software resource | Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves. | Precision recall, receiver operator characteristics, receiver operator characteristics curve, curve calculations, precision recall calculation, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN |
DOI:10.1093/bioinformatics/btw570 | Free, Freely available | biotools:precrec | https://bio.tools/precrec | SCR_018659 | 2026-08-06 09:29:21 | 1 | |||||||
|
Datanator Resource Report Resource Website 1+ mentions |
Datanator (RRID:SCR_018651) | software resource, data access protocol, application programming interface, data or information resource, web application, database | Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition. | Data discovering, cell model, model cellular biochemistry, modeling specific organism, specific environmental condition, genomics, proteomics, epigenomics, metabolomics, system biology, bio.tools |
uses: BpForms is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NIBIB P41 EB023912; NIGMS R35 GM119771 |
DOI:10.1101/2020.08.06.240051 | Free, Freely available | biotools:datanator, r3d100013339 | https://github.com/karrlab/datanator, https://bio.tools/datanator, https://doi.org/10.17616/R31NJMSB | SCR_018651 | 2026-08-06 09:29:21 | 1 | ||||||
|
Batch Web CD-Search Tool Resource Report Resource Website 100+ mentions |
Batch Web CD-Search Tool (RRID:SCR_018756) | service resource, data access protocol, web service, software resource | Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence. | Functional domain detection, protein sequence, protein sequence domain, functional domain, protein, nucleotide sequence, conserved domain search, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIH Intramural Research Program | PMID:15215404 | Free, Freely available | biotools:cd-search | https://bio.tools/cd-search | SCR_018756 | NCBI Batch CD Search Tool, Batch conserved domain search, Conserved Domain Search service, CD-search | 2026-08-06 09:29:21 | 368 | |||||
|
Vmatch Resource Report Resource Website 10+ mentions |
Vmatch (RRID:SCR_018968) | sequence analysis software, software resource, data analysis software, data processing software, software application | 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 | 2026-08-06 09:29:25 | 35 | ||||||||
|
LTR_FINDER_parallel Resource Report Resource Website 10+ mentions |
LTR_FINDER_parallel (RRID:SCR_018969) | data analysis software, software application, software resource, data processing software | Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. | Parallelization, rapid identification, retrotransposons identification, repetitive sequences, large genomes, long terminal repeat, retrotrnsposon, parallel operation, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF IOS 1740874; United States Department of Agriculture National Institute of Food ; Agriculture and AgBioResearch at Michigan State University |
PMID:31857828 | Free, Available for download, Freely available | biotools:LTR_FINDER_parallel | https://bio.tools/LTR_FINDER_parallel | SCR_018969 | 2026-08-06 09:29:30 | 14 | ||||||
|
metaXplor Resource Report Resource Website |
metaXplor (RRID:SCR_019025) | web application, data or information resource, software resource | Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures. | Data storage, metagenomics, data filtering, data sharing, data exploration, metagenomic data, viral data, microbial data, data manager, datasets sharing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Restricted | biotools:metaxplor | https://metaxplor.cirad.fr/metaXplor/, https://bio.tools/metaxplor | SCR_019025 | 2026-08-06 09:29:24 | 0 | ||||||||
|
GigaSOM.jl Resource Report Resource Website 1+ mentions |
GigaSOM.jl (RRID:SCR_019020) | data visualization software, software application, software resource, data processing software | Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets. | Flow cytometry data, flow cytometry data clustering, data clustering, data visualization, Julia, datasets, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/2020.08.03.234187 | Free, Available for download, Freely available | biotools:GigaSOM.jl | https://bio.tools/GigaSOM.jl | SCR_019020 | 2026-08-06 09:29:26 | 2 | |||||||
|
TRAL Resource Report Resource Website |
TRAL (RRID:SCR_018979) | TRAL | sequence analysis software, software resource, algorithm resource, data analysis software, data processing software, software application | Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions. | Annotation, tandem repeats annotation, amino acid repeats, nucleic data, statistical analysis, redundant predictions filtering, redundant annotation clustering, overlapping annotations clustering, false positive annotation filtering, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss State Secretariat for Education ; Research ; and Innovation |
DOI:10.1093/bioinformatics/btv306 | Free, Freely available | biotools:tral | https://bio.tools/tral | SCR_018979 | Tandem Repeat Annotation Library | 2026-08-06 09:29:30 | 0 | ||||
|
VICMpred Resource Report Resource Website 1+ mentions |
VICMpred (RRID:SCR_019039) | data access protocol, web service, software resource | Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule. | Bacterial protein, protein functional classification, virulence factor, metabolism molecule, information molecule, cellular process, gram negative bacteria, functional proteins prediction, amino acid patterns, aminoacid composition, dipeptide composition, bacterial protein sequences., bio.tools |
is listed by: Debian is listed by: bio.tools |
Council of Scientific and Industrial Research and Department of Biotechnology ; Government of India |
PMID:16689701 | Free, Freely available | biotools:vicmpred | https://bio.tools/vicmpred | SCR_019039 | Cellular process and Metabolism molecule in the bacterial proteins., Information molecule, Prediction of Virulence factors | 2026-08-06 09:29:26 | 2 | |||||
|
Annotree Resource Report Resource Website 10+ mentions |
Annotree (RRID:SCR_018980) | web service, data access protocol, data or information resource, software resource | Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes. | Genome annotation, genome visualization, phylogenetic tree, functionally annotated tree, microbial tree of life, taxonomic data, phylogenetic data, functionally annotated data, bacterial genome, archaeal genome, genome distribution, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Ontario Early Researcher award ; NSERC Discovery Grant ; Australian Research Council Laureate Fellowship ; Tier II Canada Research Chair ; Natural Sciences and Engineering Research Council of Canada |
PMID:31081040 | Free, Freely available | biotools:Annotree | https://bio.tools/AnnoTree | SCR_018980 | AnnoTree 1.2 | 2026-08-06 09:29:23 | 22 |
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