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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Indelible Resource Report Resource Website 10+ mentions |
Indelible (RRID:SCR_016163) | software application, simulation software, software resource | Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time. | indel, insertion, deletion, biological, sequence, simulation, multi-partitioned, nucleotide, amio-acid, codon, data, set, insertion, deletion, substitution, continous, time, non-homogeneous, non-stationary, phylogeny, simulator, evolution |
is listed by: Debian is listed by: OMICtools |
EPSRC/MRC Doctoral Training Centre studentship ; BBSRC |
PMID:19423664 | Free, Available for download | OMICS_15369 | https://sources.debian.org/src/indelible/ | SCR_016163 | 2026-07-27 09:35:15 | 23 | ||||||
|
Fastml Resource Report Resource Website 100+ mentions |
Fastml (RRID:SCR_016092) | web service, data access protocol, web application, software resource | Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences. | ancestral, amino-acid, sequence, reconstruction, phylogenetic, relation, accurate, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Israel Science Foundation 878/09; Bioinformatics Center at Tel-Aviv University |
PMID:22661579 | Free, Freely available | biotools:fastml, OMICS_08650 | https://bio.tools/fastml, https://sources.debian.org/src/fastml/ | SCR_016092 | The FastML Server | 2026-07-27 09:35:14 | 109 | |||||
|
Gubbins Resource Report Resource Website 500+ mentions |
Gubbins (RRID:SCR_016131) | sequence analysis software, data analysis software, software resource, software application, data processing software | Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 098051 | PMID:25414349 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_14386 | https://sources.debian.org/src/gubbins/ | SCR_016131 | Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences | 2026-07-27 09:35:15 | 602 | |||||
|
GraPhlAn Resource Report Resource Website 100+ mentions |
GraPhlAn (RRID:SCR_016130) | software application, data visualization software, software resource, data processing software | Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | circular, high, resolution, microbal, tree, taxonomy, annotation, phylogenetic, investigation |
is listed by: Debian is listed by: OMICtools has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11549 | https://huttenhower.sph.harvard.edu/graphlan, https://sources.debian.org/src/graphlan/ | SCR_016130 | Graphlan | 2026-07-27 09:35:11 | 183 | |||||||
|
Garlic Resource Report Resource Website 10+ mentions |
Garlic (RRID:SCR_016118) | data visualization software, sequence analysis software, data analysis software, software resource, software application, data processing software | Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences. | visualization, editing, biomolecule, investigation, membrane, protein, analyze, sequence |
is listed by: Debian is listed by: OMICtools |
Open source, Free, Available for download | OMICS_21303 | https://sources.debian.org/src/garlic/ | SCR_016118 | 2026-07-27 09:35:14 | 37 | ||||||||
|
Gamgi Resource Report Resource Website |
Gamgi (RRID:SCR_016116) | GAMGI | data visualization software, data analysis software, software resource, software application, data processing software | Software application which provides a graphical interface to build, view and analyze atomic structures. It provides a graphical interface to study atomic structures, to prepare images for presentations, and teach the atomic structure of matter. | gui, graphical, interface, model, atom, atomic, structure |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Runs on Linux, Tutorial available | OMICS_21302 | https://sources.debian.org/src/gamgi/ | SCR_016116 | GAMGI: General Atomistic Modelling Graphic Interface, General Atomistic Modelling Graphic Interface | 2026-07-27 09:35:14 | 0 | ||||||
|
DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | sequence analysis software, data analysis software, software resource, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
EU STREP APrIL II contract no. FP6-508861; EU NoE BIOPATTERN contract no. FP6-508803; Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind, https://sources.debian.org/src/disulfinder/ | SCR_016072 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-07-27 09:35:10 | 66 | ||||
|
DeepNano Resource Report Resource Website 1+ mentions |
DeepNano (RRID:SCR_016070) | sequence analysis software, data analysis software, software resource, software application, data processing software | Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate. | DNA, basecaller, Oxford Nanopore MinON read, sequencing, device, deep, recurrent, neural, network, accuracy, reduce, error |
is listed by: Debian is listed by: OMICtools has parent organization: Comenius University; Bratislava; Slovakia |
VEGA 1/0684/16 (BB); VEGA 1/0719/14 (TV); Slovak Research and Development Agency APVV-14-0253; NVIDIA Corporation |
PMID:28582401 | Free, Available for download | OMICS_14561 | http://compbio.fmph.uniba.sk/deepnano/, https://sources.debian.org/src/deepnano/ | SCR_016070 | DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads, DeepNano: alternative basecaller for MinION reads | 2026-07-27 09:35:13 | 4 | |||||
|
Falcon Resource Report Resource Website 100+ mentions |
Falcon (RRID:SCR_016089) | image analysis software, software resource, software application, alignment software, data processing software | Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes. | fast, aligner, sequencing, diploid, genome, assembly, non-inbred, rearranged, heterozygous, single-molecule |
is listed by: Debian is listed by: OMICtools is related to: Howard Hughes Medical Institute |
National Science Foundation DBI-1350041; National Science Foundation IOS-1237880; National Science Foundation MCB 0929402; National Science Foundation MCB 1122246; Gordon and Betty Moore Foundation GBMF 3034; NHGRI R01 HG006677 |
PMID:27749838 | Free, Available for download, Freely available | OMICS_13514 | https://sources.debian.org/src/falcon/ | SCR_016089 | 2026-07-27 09:35:14 | 279 | ||||||
|
Gff2aplot Resource Report Resource Website |
Gff2aplot (RRID:SCR_016128) | software application, data visualization software, data processing software, software resource | Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis. | alignment, pair-wise, plot, genomic, sequence, visualize, together, annotate, analysis, parameter, dataset, |
is listed by: Debian is listed by: OMICtools |
PMID:14668236 | Free, Available for download | OMICS_19949 | https://sources.debian.org/src/gff2aplot/ | SCR_016128 | 2026-07-27 09:35:15 | 0 | |||||||
|
Gentle Resource Report Resource Website 1+ mentions |
Gentle (RRID:SCR_016127) | sequence analysis software, data analysis software, software resource, software application, data processing software, software toolkit | Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. | editing, database, management, plasmid maps, restriction, ligation, alignments, sequence, data, import, calculator, gel, image, display, PCR, cloning, genetic |
is listed by: Debian is listed by: OMICtools has parent organization: University of Cologne; Cologne; Germany |
Free Software Foundation | Free, Available for download | OMICS_18307 | https://sources.debian.org/src/gentle/ | SCR_016127 | GENtle | 2026-07-27 09:35:11 | 6 | ||||||
|
PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | software application, software resource, data processing software, data analysis software | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-07-27 09:35:31 | 15 | ||||||||
|
Phangorn Resource Report Resource Website 10+ mentions |
Phangorn (RRID:SCR_017302) | data visualization software, data analysis software, software resource, software application, data processing software, software toolkit | Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks. | phylogenetic, tree, network, reconstruction, analysis, estimation, Maximum, Likelihood, Parsimony, distance, method, Hadamard conjugation |
is listed by: Debian is listed by: OMICtools is related to: CRAN |
Muséum National D Histoire Naturelle | DOI:10.1093/bioinformatics/btq706 | Free, Available for download, Freely available | OMICS_12497 | https://github.com/KlausVigo/phangorn, https://sources.debian.org/src/r-cran-phangorn/ | SCR_017302 | Phangorn R package | 2026-07-27 09:35:28 | 24 | |||||
|
BioAssay Express Resource Report Resource Website |
BioAssay Express (RRID:SCR_017594) | web service, service resource, data access protocol, software resource | Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations. | Annotating, bioassay, protocol, semantic, web, term, ontology | is listed by: OMICtools | NCATS R44 TR000185 | DOI:10.7717/peerj-cs.61 | Free, Freely available | https://github.com/cdd/bioassay-template | SCR_017594 | 2026-07-27 09:35:34 | 0 | |||||||
|
GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | software application, software resource, data processing software, data analysis software | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-07-27 09:35:33 | 3 | |||||
|
GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | atlas, service resource, data analysis service, database, analysis service resource, production service resource, data or information resource | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | Gene ATLAS, Gene Atlas | 2026-07-27 09:35:42 | 132 | |||||||||
|
immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | service resource, software resource, software application, text-mining software, data or information resource | Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. | Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract |
is listed by: NIDDK Information Network (dkNET) is listed by: OMICtools |
NIH ; NIAID ; Rappaport Family Institute for Research in the Medical Sciences |
PMID:29912209 | Free, Freely available | SCR_017578 | 2026-07-27 09:35:31 | 0 | ||||||||
|
Bustools Resource Report Resource Website 10+ mentions |
Bustools (RRID:SCR_018210) | software application, software resource, data processing software, data analysis software | Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. | Single cell RNAseq workflow, single cell RNAseq dataset, error correct barcode, collapse UMI, produce gene count, produce transcript compatibility count matrice |
is listed by: Debian is listed by: OMICtools works with: kb_python |
DOI:10.1101/673285 | Free, Available for download, Freely available | OMICS_33004 | https://sources.debian.org/src/bustools/ | SCR_018210 | 2026-07-27 09:35:42 | 18 | |||||||
|
ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | software application, software resource, data processing software, data analysis software | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-07-27 09:35:41 | 47 | ||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | image analysis software, software resource, software application, alignment software, data processing software | 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 | 2026-07-27 09:35:45 | 1325 |
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