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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MUMmer Resource Report Resource Website 100+ mentions |
MUMmer (RRID:SCR_018171) | software resource, image analysis software, alignment software, data processing software, software application | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NLM R01 LM06845; NSF IIS 9902923; NIAID N01 AI15447 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-08-06 09:29:20 | 480 | |||||
|
GeneMarkS-T Resource Report Resource Website 100+ mentions |
GeneMarkS-T (RRID:SCR_017648) | data analysis software, software application, software resource, data processing software | Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. | Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Georgia Institute of Technology; Georgia; USA |
NHGRI HG000783 | PMID:25870408 | Restricted | biotools:GeneMarkS-t | https://bio.tools/GeneMarkS-T | SCR_017648 | 2026-08-06 09:29:07 | 113 | ||||||
|
NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | data access protocol, web service, software resource | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan, https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ | SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-08-06 09:29:18 | 138 | |||||
|
Mousebytes Resource Report Resource Website 1+ mentions |
Mousebytes (RRID:SCR_017904) | storage service resource, service resource, data repository, data or information resource, database | Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available. | Data, mouse, cognition, imaging, genomics, integration, bio.tools, OpenBehavior |
is listed by: Debian is listed by: bio.tools is listed by: OpenBehavior has parent organization: Western University; Ontario; Canada |
Weston Brain Institute (Canada) ; Canadian Institute of Health Research ; NSERC ; Alzheimer’s Society of Canada ; Canadian First Research Excellence Fund (BrainsCAN) ; Brain Canada |
PMID:31825307 | Free, Freely available | SCR_021549, SCR_021598, r3d100013886, biotools:Mousebytes | https://bio.tools/MouseBytes, https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/, https://doi.org/10.17616/R31NJN7I | SCR_017904 | MouseBytes | 2026-08-06 09:29:16 | 4 | |||||
|
4See Resource Report Resource Website 1+ mentions |
4See (RRID:SCR_018014) | data visualization software, software application, software resource, data processing software | Software tool to visualize 4C data. | Visualize, 4C data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.3389/fgene.2019.01372 | Free, Available for download, Freely available | biotools:4see | https://bio.tools/4see | SCR_018014 | 2026-08-06 09:29:19 | 1 | |||||||
|
NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software resource, data analysis software, software toolkit, data processing software, software application | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-08-06 09:29:19 | 2 | |||||
|
Online Peri-Event Time Histogram for Open Ephys Resource Report Resource Website 1+ mentions |
Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) | OPETH | data visualization software, software application, software resource, data processing software | Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them. | Open source, open ephys, optogenetics, behavior, electrophysiology data, neuroscience experiment, spike detection, behavior tagging, neuron, histogram, bio.tools |
is listed by: Debian is listed by: bio.tools |
Hungarian Academy of Sciences Lendület Program LP2015-2/2015; European Research Council Starting Grant 715043; Generalitat Valenciana Postdoctoral Fellowship Program APOSTD/2019/003 |
DOI:10.1101/783688 | Free, Available for download, Freely available | biotools:OPEtH | https://bio.tools/OPETH | SCR_018022 | Online Peri-Event Time Histogram | 2026-08-06 09:29:16 | 4 | ||||
|
ΔG prediction server Resource Report Resource Website 10+ mentions |
ΔG prediction server (RRID:SCR_018191) | service resource, data access protocol, web service, software resource | Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon. | Amino acid sequence, putative transmembrane helix, free energy difference, sequence insertion, endoplasmic reticulum membrane, potential TM helix, predict energy difference, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stockholm University; Stockholm; Sweden |
Free, Freely available | biotools:deltag_prediction | http://dgpred.cbr.su.se/index.php?p=TMpred, https://bio.tools/deltag_prediction | SCR_018191 | ΔG prediction server v1.0 | 2026-08-06 09:29:21 | 12 | |||||||
|
BioNix Resource Report Resource Website 1+ mentions |
BioNix (RRID:SCR_017662) | software library, software toolkit, software resource | Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language. | Workflow, engine, package, manager, container, unify, bioinformatics, Nix, functional, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:bioNix | https://bio.tools/BioNix | SCR_017662 | 2026-08-06 09:29:07 | 4 | ||||||||
|
Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | software resource, data analysis software, data processing software, data visualization software, software application | Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org, https://bio.tools/mvp_a | SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-08-06 09:29:19 | 1 | |||||
|
PEMA Resource Report Resource Website 1+ mentions |
PEMA (RRID:SCR_017676) | software resource, data analysis software, software toolkit, data processing software, software application | Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution. | Environmental, DNA, metabarcoding, analysis, ASVs, OTUs, 16S rRNA, COI, ITS, marker, gene, clustering, taxonomy, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/709113 | Free, Freely available | biotools:PEMA | https://docs.google.com/presentation/d/1lVH23DPa2NDNBhVvOTRoip8mraw8zfw8VQwbK4vkB1U/edit?fbclid=IwAR14PpWfPtxB8lLBBnoxs7UbG3IJfkArrJBS5f2kRA__kvGDUb8wiJ2Cy_s#slide=id.g57f092f54d_1_21, https://bio.tools/PEMA | SCR_017676 | Pipeline for Environmental DNA Metabarcoding Analysis | 2026-08-06 09:29:07 | 1 | ||||||
|
DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-08-06 09:29:14 | 62 | ||||||
|
ProtParam Tool Resource Report Resource Website 5000+ mentions |
ProtParam Tool (RRID:SCR_018087) | sequence analysis software, software resource, service resource, production service resource, data analysis software, data processing software, software application, analysis service resource | Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. | Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal |
NHGRI U01 HG02712; Swiss Federal Government through Federal Office of Education and Science |
PMID:10027275 | Free, Freely available | biotools:protparam | https://bio.tools/protparam | SCR_018087 | ProtParam | 2026-08-06 09:29:19 | 5406 | |||||
|
biospytial Resource Report Resource Website 1+ mentions |
biospytial (RRID:SCR_018226) | software resource, data analysis software, data management software, software toolkit, data processing software, data visualization software, software application | Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system. | spatial data infrastructure, biodiversity informatics, ecological knowledge engine, ecological data analysis, biodiversity, taxonomic classification, bio.tools |
is listed by: Debian is listed by: bio.tools |
CONACyT ; GBIF ; Lancaster University |
DOI:10.5524/100723 | Free, Available for download, Freely available | biotools:biospytial | https://bio.tools/biospytial | SCR_018226 | 2026-08-06 09:29:22 | 2 | ||||||
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Plant Co-expression Annotation Resource Resource Report Resource Website 1+ mentions |
Plant Co-expression Annotation Resource (RRID:SCR_018429) | Plantannot | software resource, service resource, data access protocol, web service, data or information resource | Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard. | Omics, plant, annotation, function, breeding, genetically modified crops, abiotic stress in plant, plant genome, plant genomic data, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Phytozome is related to: NCBI is related to: Machado |
Embrapa | DOI:10.1101/2020.05.22.110510 | Free, Freely available | biotools:plantannot | https://www.machado.cnptia.embrapa.br/plantannot2, https://bio.tools/plantannot | SCR_018429 | Plantannot v2 | 2026-08-06 09:29:19 | 1 | ||||
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pepwheel Resource Report Resource Website 1+ mentions |
pepwheel (RRID:SCR_018398) | service resource, data access protocol, web service, software resource | Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation. | Computational proteomics, data analysis pipeline, label free quantification, mass spectrometry, quantitative proteomics, visualise protein sequence, helical wheel diagram, peptice sequence display, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: EMBOSS works with: Proteome Discoverer |
Free, Freely available | biotools:pepwheel | https://bio.tools/pepwheel | SCR_018398 | 2026-08-06 09:29:19 | 1 | ||||||||
|
TDimpute Resource Report Resource Website 1+ mentions |
TDimpute (RRID:SCR_018306) | data analysis software, software application, software resource, data processing software | Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data. | Transfer learning; gene expression prediction; DNA methylation; TCGA, neural network, missing gene expression, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/803692 | Free, Available for download, Freely available | biotools:tDimpute, BioTools:TDimpute | https://bio.tools/TDimpute, https://bio.tools/TDimpute, https://bio.tools/TDimpute | SCR_018306 | 2026-08-06 09:29:23 | 1 | |||||||
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betaVAEImputation Resource Report Resource Website 1+ mentions |
betaVAEImputation (RRID:SCR_018730) | data analysis software, software application, software resource, data processing software | Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis. | Genomic data, handling missing data, deep learning framework, variational autoencoder, imputing missing values, transcriptome, methylome, data analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:betavaeimputation | https://bio.tools/betavaeimputation | SCR_018730 | 2026-08-06 09:29:21 | 2 | ||||||||
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Protein Interactions Calculator Resource Report Resource Website 10+ mentions |
Protein Interactions Calculator (RRID:SCR_018574) | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex. | Protein interaction, interaction calculation, single site, accessible surface are, residue depth, protein surface, residue distance, residue interaction, protein complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Department of Biotechnology Government of India | PMID:17584791 | Free, Freely available | biotools:pic | https://bio.tools/pic | http://crick.mbu.iisc.ernet.in/~PIC | SCR_018574 | 2026-08-06 09:29:20 | 27 | |||||
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LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | software resource, data access protocol, service resource, production service resource, web service, analysis service resource | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIEHS P30 ES06096; NIEHS U01 ES015675; NHGRI R01 HG003749; NLM R01 LM008106; NIDA U54 DA021519 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | 2026-08-06 09:29:28 | 4 |
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