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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MeroX Resource Report Resource Website 50+ mentions |
MeroX (RRID:SCR_014956) | sequence analysis software, data processing software, data analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links. | sequence analysis software, cross linking, mass spectrometry, MS cleavage, fragmentation, cleavable cross link, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: StavroX |
PMID:25261217 | THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:MeroX, biotools:MeroX | https://bio.tools/MeroX https://bio.tools/MeroX https://bio.tools/MeroX |
SCR_014956 | 2026-02-14 02:02:45 | 74 | |||||||
|
BUSCO Resource Report Resource Website 5000+ mentions |
BUSCO (RRID:SCR_015008) | data processing software, data analysis software, software application, software resource, algorithm resource | Software tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. | genome assembly, annotation completeness, quantitative method, bio.tools |
is used by: rnaQUAST is recommended by: CEGMA is listed by: Debian is listed by: bio.tools is related to: CEGMA works with: BUSCOMP |
Swiss National Science Foundation ; Marie Curie International Outgoing Fellowship |
DOI:10.1093/bioinformatics/btv351 | Free, Available for download, Freely available | biotools:busco | https://gitlab.com/ezlab/busco https://bio.tools/busco https://sources.debian.org/src/busco/ |
SCR_015008 | BUSCO v2, Benchmarking Universal Single-Copy Orthologs (BUSCO), Benchmarking Universal Single-Copy Orthologs, BUSCO v1 | 2026-02-14 02:03:04 | 7284 | |||||
|
LTR_Finder Resource Report Resource Website 500+ mentions |
LTR_Finder (RRID:SCR_015247) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web software capable of scanning large-scale sequences for full-length LTR retrotranspsons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Long Terminal Repeat retrotransposons, Long Terminal Repeat, retrotransposon prediction, genome sequences, LTR prediction, LTR structure prediction, DNA sequence, biotools |
is listed by: Debian is listed by: bio.tools |
Fudan University ; Shanghai ; China |
PMID:17485477 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_020944, biotools:ltr_finder | https://bio.tools/ltr_finder | SCR_015247 | LTR Finder | 2026-02-14 02:03:01 | 795 | |||||
|
fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:28 | 23 | |||||||
|
ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | web service, analysis service resource, production service resource, service resource, data access protocol, software 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 | 2026-02-14 02:03:17 | 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 | 2026-02-14 02:03:34 | 1 | |||||||
|
SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:28 | 2 | ||||||
|
CRISPRdirect Resource Report Resource Website 100+ mentions |
CRISPRdirect (RRID:SCR_018186) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. | CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Japan Science and Technology Agency ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:25414360 | Free, Freely available | biotools:CRISPRdirect | https://bio.tools/CRISPRdirect | SCR_018186 | 2026-02-14 02:03:28 | 452 | ||||||
|
Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | software resource, workflow software, data processing software, software application | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 81573023 ; National Key Research and Development Program 2017YFC0908500 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-02-14 02:03:30 | 2 | |||||
|
HingeProt Resource Report Resource Website 1+ mentions |
HingeProt (RRID:SCR_018136) | data access protocol, software resource, web service, service resource | Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures. | Predicting protein hinges, flexible hinge region, native topology, rigid protein part, elastic network model, protein structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17847101 | Free, Available for download, Freely available | biotools:hingeprot | https://bio.tools/hingeprot | SCR_018136 | 2026-02-14 02:03:17 | 4 | |||||||
|
Warp Resource Report Resource Website 1+ mentions |
Warp (RRID:SCR_018071) | data processing software, data acquisition software, data analysis software, software application, software resource | Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising. | Automating preprocessing step, cryo EM data acquisition, micrograph correction, particle picking, image denoising, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1038/s41592-019-0580-y | Free, Available for download, Freely available | BioTools:Warp, biotools:Warp | https://bio.tools/Warp https://bio.tools/Warp https://bio.tools/Warp |
SCR_018071 | 2026-02-14 02:03:16 | 7 | |||||||
|
RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | web service, software application, data access protocol, software resource, simulation software | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | 2026-02-14 02:03:27 | 149 | ||||||
|
CLIP-Explorer Resource Report Resource Website 1+ mentions |
CLIP-Explorer (RRID:SCR_018128) | data visualization software, data processing software, data analysis software, service resource, software application, software resource | Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP. | CLIP-seq data, RNA protein interaction, Galaxy, data analysis, eCLIP, iCLIP, FLASH, uvCLAP, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: FLASH |
Restricted | SCR_018130, biotools:CLIP-Explorer | https://bio.tools/CLIP-Explorer | SCR_018128 | 2026-02-14 02:03:31 | 2 | ||||||||
|
PlotTwist Resource Report Resource Website 10+ mentions |
PlotTwist (RRID:SCR_018331) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web application for plotting and annotating continuous data. Open source web app for plotting and annotating time series data. Used to inspect data and generate publication quality visualizations. Available options for plotting include lineplot, small multiples and heatmap, summary statistics and inferential statistics. | Plotting continuous data, annotating continuous data, data visualization, time series data, line plot, small multiples, heatmap, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31929523 | Free, Freely available | biotools:Plottwist, BioTools:PlotTwist | https://github.com/JoachimGoedhart/PlotTwist https://bio.tools/PlotTwist https://bio.tools/PlotTwist https://bio.tools/PlotTwist |
SCR_018331 | PlotTwist Shiny | 2026-02-14 02:03:19 | 10 | ||||||
|
CRISPRcasIdentifier Resource Report Resource Website 1+ mentions |
CRISPRcasIdentifier (RRID:SCR_018296) | data analysis software, software resource, data processing software, software application | Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes. | CRISPR-Cas, Machine Learning, Cas genes, Cas proteins, input protein cassette, predicting subtype, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/817619 | Free, Available for download, Freely available | biotools:crisprcasidentifier | https://bio.tools/crisprcasidentifier | SCR_018296 | 2026-02-14 02:03:19 | 4 | |||||||
|
SymPy Resource Report Resource Website 1+ mentions |
SymPy (RRID:SCR_018417) | software resource, software library, software toolkit | Software Python library for symbolic mathematics. It aims to become full featured computer algebra system (CAS) while keeping code as simple as possible in order to be comprehensible and easily extensible. | Python, Python library, symbolic mathematics, computer algebra system, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:SymPy | https://bio.tools/SymPy | SCR_018417 | 2026-02-14 02:03:20 | 9 | ||||||||
|
smashpp Resource Report Resource Website 1+ mentions |
smashpp (RRID:SCR_018307) | data visualization software, data processing software, data analysis 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++ | 2026-02-14 02:03:33 | 2 | |||||||
|
GPS-SUMO Resource Report Resource Website 1+ mentions |
GPS-SUMO (RRID:SCR_018261) | web service, portal, data or information resource, service resource, data access protocol, software resource | 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 |
National Natural Science Foundation of China ; National Basic Research Program ; Guangdong Natural Science Funds for Distinguished Young Scholar ; Zhujiang Nova Program of Guangzhou ; International Science and Technology Cooperation Program of China |
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 | 2026-02-14 02:03:33 | 2 | |||||
|
NanoSim Resource Report Resource Website 10+ mentions |
NanoSim (RRID:SCR_018243) | software resource, simulation software, software application | Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software. | Nanopore sequence read, sequence simulator, Oxford Nanopore Technology, next generation sequencing, long nanopore read, genome assembly, mutation detection, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI R01 HG007182; Genome Canada ; Genome British Columbia ; British Columbia Cancer Foundation ; University of British Columbia |
DOI:10.1093/gigascience/gix010 | Free, Available for download, Freely available | biotools:trans-nanosim, biotools:nanosim | https://www.bcgsc.ca/resources/software/nanosim https://bio.tools/nanosim https://bio.tools/Trans-NanoSim |
SCR_018243 | 2026-02-14 02:03:32 | 18 | ||||||
|
SpoTyping Resource Report Resource Website 10+ mentions |
SpoTyping (RRID:SCR_018466) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:03:38 | 10 |
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