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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
smashpp Resource Report Resource Website 1+ mentions |
smashpp (RRID:SCR_018307) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool to find and visualize rearrangements in DNA sequences. | Find sequence rearrangement, visualize sequence rearrangement, DNA, DNA sequence, DNA sequence rearrangement, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:smashpp, BioTools:smashpp | https://bio.tools/smashpp, https://bio.tools/smashpp, https://bio.tools/smashpp | SCR_018307 | Smash++ | 2026-09-12 12:58:59 | 2 | |||||||
|
GPS-SUMO Resource Report Resource Website 1+ mentions |
GPS-SUMO (RRID:SCR_018261) | data access protocol, data or information resource, portal, service resource, software resource, web service | Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup. | Small ubiquitin like modifier, SUMOs, sumoylation, covalently modified protein, group prediction system, site prediction, interaction motif in protein, bio.tools |
is listed by: Debian is listed by: bio.tools |
Guangdong Natural Science Funds for Distinguished Young Scholar ; International Science and Technology Cooperation Program of China ; National Basic Research Program ; National Natural Science Foundation of China ; Zhujiang Nova Program of Guangzhou |
PMID:24880689 | Restricted | biotools:gps-sumo | http://sumosp.biocuckoo.org/online.php, https://bio.tools/gps-sumo | SCR_018261 | Group-based Prediction System -Small Ubiquitin-like MOdifiers, Small Ubiquitin-like MOdifiers sp, GPS-SUMO 2.0, SUMOsp, GPS Small Ubiquitin-like MOdifiers, Group-based Prediction System-SUMO | 2026-09-12 12:58:59 | 6 | |||||
|
SpoTyping Resource Report Resource Website 10+ mentions |
SpoTyping (RRID:SCR_018466) | data analysis software, data processing software, software application, software resource | Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads. | bio.tools |
is listed by: bio.tools is listed by: Debian |
National University of Singapore ; Singapore ; Singapore |
DOI:10.1186/s13073-016-0270-7 | Free, Available for download, Freely available | biotools:spotyping | https://bio.tools/spotyping | SCR_018466 | SpoTyping-v2.0, SpoTyping | 2026-09-12 12:59:01 | 12 | |||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2, https://sources.debian.org/src/libminimap2-dev/ | SCR_018550 | 2026-09-12 12:59:02 | 1593 | ||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data processing software, data visualization software, software application, software resource | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-09-12 12:59:02 | 61 | ||||||
|
DAMBE Resource Report Resource Website 10+ mentions |
DAMBE (RRID:SCR_018528) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. | Data analysis, molecular sequence data, genomic data, phylogenetic data, data, anaysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Ottawa; Ontario; Canada |
Hong Kong Research Grant Council ; Natural Science and Engineering Research Council of Canada ; University of Hong Kong |
PMID:11535656 PMID:28379490 PMID:23564938 PMID:29669107 |
Free, Available for download, Freely available | biotools:dampe | https://bio.tools/dambe | SCR_018528 | DAMBE6, DAMBE5, DAMBE7, Data Analysis in Molecular Biology and Evolution | 2026-09-12 12:59:02 | 12 | |||||
|
EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIAID P30 AI027757; NIAID P30 AI050409; NICHD R01 HD068395; NICHD R21 HD075662; NICHD T32 HD007543; NIDA P30 DA027828; NIMH R21 MH112449 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-09-12 12:59:02 | 8 | ||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software application, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-09-12 12:59:02 | 46 | ||||||
|
Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | application programming interface, data access protocol, data or information resource, software resource, web service | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | 2026-09-12 12:59:01 | 2 | |||||||
|
ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling. | Protein structure, protein, protein structure refinement, protein structure validation, protein structure prediction, protein structure modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
FWF Austria ; University of Salzburg ; Austria. |
PMID:17517781 | Free, Freely available | biotools:prosa-web | https://bio.tools/prosa-web | SCR_018540 | Protein Structure Analysis web | 2026-09-12 12:59:02 | 109 | |||||
|
Graph2GO Resource Report Resource Website 1+ mentions |
Graph2GO (RRID:SCR_018726) | data analysis software, data processing software, software application, software resource | Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology. | Protein function prediction, graph neural network, attributed network embedding, representation learning, multi-modal model, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ohio State University College of Medicine; Ohio; USA |
Free, Available for download, Freely available | SCR_018727, biotools:graph2go | https://integrativeomics.shinyapps.io/graph2go/, https://bio.tools/graph2go | SCR_018726 | 2026-09-12 12:59:05 | 2 | ||||||||
|
BioSimulations Resource Report Resource Website 1+ mentions |
BioSimulations (RRID:SCR_018733) | software resource, web application | Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell. | Sharing, reusing, biomodel, simulation, visualization, simulation result, modeling framework support, simulation tool support, model format support, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA has parent organization: University of Connecticut; Connecticut; USA |
NIBIB P41 EB023912; NIGMS ; NSF |
Restricted | biotools:biosimulations | https://bio.tools/biosimulations | SCR_018733 | 2026-09-12 12:59:05 | 1 | |||||||
|
rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. | Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools |
is listed by: Debian is listed by: bio.tools works with: TRANSFAC |
PMID:15215384 | Free, Freely available | biotools:rvista | https://bio.tools/rvista | SCR_018707 | rVista 2.0 | 2026-09-12 12:59:05 | 34 | ||||||
|
BpForms Resource Report Resource Website |
BpForms (RRID:SCR_018653) | data access protocol, software resource, software toolkit, web service | Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. | Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools |
uses: BcForms is used by: ObjTables is used by: Datanator is listed by: Debian is listed by: bio.tools is related to: BcForms is related to: ObjTables |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bpforms | https://bio.tools/bpforms | SCR_018653 | 2026-09-12 12:59:04 | 0 | ||||||
|
ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data management software, data processing software, software application, software resource, software toolkit | Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. | Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools |
uses: BpForms uses: BcForms is listed by: bio.tools is listed by: Debian is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | 2026-09-12 12:59:04 | 0 | |||||||
|
Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq, https://bio.tools/preseq | SCR_018664 | 2026-09-12 12:59:04 | 21 | |||||||
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data analysis software, data processing software, network analysis software, software application, software resource, software toolkit | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | Mutual Information NETworks | 2026-09-12 12:59:04 | 0 | |||||
|
MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, service resource, software resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCATS UL1 TR001114; NCI K22 CA188163; NHGRI U01 HG006476; NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info, https://bio.tools/mygene.info, https://bio.tools/mygene.info | SCR_018660 | 2026-09-12 12:59:04 | 34 | ||||||
|
DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-09-12 12:58:40 | 6 | ||||
|
MentaLiST Resource Report Resource Website 10+ mentions |
MentaLiST (RRID:SCR_016469) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome BC ; Genome Canada |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-09-12 12:58:40 | 15 |
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