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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Codon Usage Analyzer Resource Report Resource Website |
Codon Usage Analyzer (RRID:SCR_018500) | Bio::CUA, Bio-CUA | software application, software resource, data analysis software, data processing software | Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems. | Codon usage analyzer, codon, codon usage bias, genome, gene, codon, sequence | has parent organization: University of Rochester; New York; USA | David and Lucile Packard Foundation ; University of Rochester |
DOI:10.1101/022814 | Free, Freely available | https://metacpan.org/release/Bio-CUA | SCR_018500 | 2026-07-28 09:44:41 | 0 | ||||||
|
rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | 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 | 2026-07-28 09:44:44 | 30 | ||||||
|
FunCoup Resource Report Resource Website 1+ mentions |
FunCoup (RRID:SCR_018711) | service resource, data or information resource, database, data access protocol, software resource, web service | Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search. | Genome, genome functional coupling network, coupling network, functional coupling, functional couplings search, gene identifier, genome data | has parent organization: Karolinska Institute; Stockholm; Sweden | Swedish Research Council ; Stockholm University |
PMID:24185702 | Free, Freely available | SCR_018711 | 2026-07-28 09:44:44 | 3 | ||||||||
|
Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | software application, data analysis software, software resource, data processing software, 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 | 2026-07-28 09:44:43 | 19 | |||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data or information resource, database, data access protocol, software resource, web service | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-07-28 09:44:53 | 233 | |||||||
|
Differential Methylation Analysis Package Resource Report Resource Website |
Differential Methylation Analysis Package (RRID:SCR_019148) | DMAP | software application, data analysis software, software resource, data processing software, software toolkit | Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity. | Genomic DNA methylation, DNA methylation analysis, bisulphite sequenced data, reference methylomes generation, genome, aligned SAM files processing, differentially methylated regions | has parent organization: University of Otago; Dunedin; New Zealand | National Centre for Growth and Development and Health Research Council ; New Zealand |
PMID:24608764 | Free, Freely available | SCR_019148 | 2026-07-28 09:44:57 | 0 | |||||||
|
OMA Orthology database Resource Report Resource Website 1+ mentions |
OMA Orthology database (RRID:SCR_016425) | OMA | software application, data or information resource, database, data access protocol, software resource, web service, standalone software | Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | interface, orthology, prediction, inference, complete, genome, species, data | Swiss Institute of Bioinformatics ; UK Biotechnology and Biological Sciences Research Council ; University College London ; Bayer Crop Science NV |
PMID:29106550 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016425 | Orthologous MAtrix | 2026-07-28 09:44:17 | 9 | |||||||
|
RNA22 Resource Report Resource Website 100+ mentions |
RNA22 (RRID:SCR_016507) | RNA22 | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases. | pattern, based, detecting, microRNA, binding, site, complex, sequence, genome, analysis, FASEB list | is listed by: OMICtools | A Star ; Singapore ; NIDDK DK04763; NIH AI54973 |
Free, Available for download, Freely available | SCR_016507 | RiboNucleic Acid 22 | 2026-07-28 09:44:19 | 192 | |||||||
|
MetaPGN Resource Report Resource Website 1+ mentions |
MetaPGN (RRID:SCR_016472) | MetaPGN | software application, data analysis software, software toolkit, software resource, data processing software, data visualization software, network graph visualization software | Pipeline for construction and graphical visualization of annotated pangenome networks from microbial genomes. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data provides pangenome analysis to uncultured microbial taxa., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | construct, graphical, visualization, annotated, pangenome, network, microbal, genome, metagenome | PMID:30277499 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/peng-ye/MetaPGN | SCR_016472 | Meta PanGeNome | 2026-07-28 09:44:18 | 2 | |||||||
|
NCBI Biocollections Resource Report Resource Website 1+ mentions |
NCBI Biocollections (RRID:SCR_016459) | NCBI Biocollections | software application, data or information resource, organization portal, database, data processing software, software resource, registration software, image analysis software, portal | Registry of bio-collections linked to genomes. Collection of curated dataset of metadata for culture collections, museums, herbaria and other natural history collections, including Darwin Core institution and collection codes, and URL formulae for mapping specimen ids to web pages at the collection site. | registry, biocollection, linked, genome, dataset, metadata | SCR_016459 | NCBI Biocollections:National Center for Biotechnology Information Biocollections | 2026-07-28 09:44:19 | 1 | ||||||||||
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MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | software application, data analysis software, sequence analysis software, software resource, data processing software | 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 Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-07-28 09:44:18 | 8 | ||||||
|
fermi Resource Report Resource Website |
fermi (RRID:SCR_016652) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes. | assembler, analysis, whole, genome, short, gun, sequencing, error, correction | is listed by: OMICtools | NHGRI U01 HG005208 | PMID:22569178 | Free, Available for download, Freely available | SCR_016652 | 2026-07-28 09:44:24 | 0 | ||||||||
|
CheckM Resource Report Resource Website 100+ mentions |
CheckM (RRID:SCR_016646) | software application, data analysis software, software resource, data processing software, software toolkit | Software tool to assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes by using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. | assess, quality, microbial, genome, recovered, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/gr.186072.114 | Free, Available for download, Freely available | biotools:checkm | https://github.com/Ecogenomics/CheckM, https://bio.tools/checkm | SCR_016646 | 2026-07-28 09:44:20 | 184 | |||||||
|
TRIAGE Resource Report Resource Website 1+ mentions |
TRIAGE (RRID:SCR_016609) | TRIAGE | service resource, web application, data analysis service, software resource, production service resource, analysis service resource | Platform to facilitate prediction, analysis, and hypothesis generation from genome wide perturbation studies like those designed with RNAi and CRISPR technologies. | prediction, analysis, hypothesis, generation, genome, perturbation, study, RNAi, CRISP | is listed by: NIAID | NIH | Free, Available for download, Freely available | SCR_016609 | Throughput Ranking by Iterative Analysis of Genomic Enrichment | 2026-07-28 09:44:23 | 1 | |||||||
|
KAT Resource Report Resource Website 10+ mentions |
KAT (RRID:SCR_016741) | KAT | software application, data analysis software, software resource, data processing software, software toolkit | Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies. | generate, analyse, compare, k-mer, spectra, sequence, file, quality, control, NGS, dataset, genome, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC | DOI:10.1093/bioinformatics/btw663 | Free, Available for download, Freely available | biotools:kat | http://www.earlham.ac.uk/kat-tools, https://bio.tools/kat | SCR_016741 | K-mer Analysis Toolkit | 2026-07-28 09:44:24 | 19 | ||||
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Flye Resource Report Resource Website 100+ mentions |
Flye (RRID:SCR_017016) | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Software package as de novo assembler for single molecule sequencing reads. Used for assembling long, error prone reads such as those produced by PacBio and Oxford Nanopore Technologies, for fast and accurate genome reconstructions. Available for Linux and MacOS platforms. | assembler, single, molecule, sequencing, long, error, read, fast, accurate, genome, reconstruction, nucleotide, quality, data, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at San Diego; California; USA |
PMID:27956617 | Free, Available for download, Freely available | biotools:Flye | https://bio.tools/Flye, https://sources.debian.org/src/flye/ | SCR_017016 | 2026-07-28 09:44:30 | 267 | |||||||
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BBmap Resource Report Resource Website 500+ mentions |
BBmap (RRID:SCR_016965) | software application, software toolkit, software resource, data processing software, alignment software, image analysis software | Software tool as a short read aligner for DNA and RNA seq data. Used for large genomes with millions of scaffolds. Can align reads from Illumina, PacBio, 454, Sanger, Ion Torrent, Nanopore. Fast and accurate, particularly with highly mutated genomes or reads with long indels, even whole gene deletions over 100kbp long. It has no upper limit to genome size or number of contigs. Written in Java, can run on any platform. | Joint Genome Institute, short, read, aligner, DNA, RNA, sequencing, data, large, genome, scaffold, mutated, long, indel |
is listed by: Bestus Bioinformaticus Tools is listed by: Debian is related to: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/, https://sources.debian.org/src/bbmap/ | SCR_016965 | 2026-07-28 09:44:25 | 797 | |||||||||
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TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | software application, data analysis software, software resource, data processing software, software toolkit | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Arnold and Mabel Beckman foundation ; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-07-28 09:44:27 | 10 | ||||||
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Maize Database of Images and Genomes Resource Report Resource Website 1+ mentions |
Maize Database of Images and Genomes (RRID:SCR_016987) | MaizeDIG | service resource, data or information resource, database, production service resource, analysis service resource | Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name. | genotype, phenotype, collection, maize, image, reference, genome | works with: MaizeGDB | Free, Freely available | SCR_016987 | Maize Dig, MaizeDatabase of Images and Genomes, MaizeDig, MaizeDIG | 2026-07-28 09:44:30 | 5 | ||||||||
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SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | software application, software resource, data analysis software, data processing software | Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets. | orthology, analysis, identify, ortholog, paralog, co ortholog, genome, homology, different, species, large, dataset, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/543223 | Free, Available for download, Freely available | OMICS_30890, biotools:SwiftOrtho | https://bio.tools/SwiftOrtho | SCR_017122 | 2026-07-28 09:44:31 | 4 |
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