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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ATRHUNTER Resource Report Resource Website 1+ mentions |
ATRHUNTER (RRID:SCR_006480) | ATRHUNTER | software resource, service resource, production service resource, data analysis service, analysis service resource | Software that finds and displays approximate tandem repeats in DNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16201913 | biotools:atrhunter, OMICS_00102 | https://bio.tools/atrhunter | SCR_006480 | 2026-08-06 09:26:35 | 1 | |||||||
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LAST Resource Report Resource Website 100+ mentions |
LAST (RRID:SCR_006119) | LAST | software resource, service resource, production service resource, data analysis service, data processing software, software application, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence alignment, align, vertebrate, genome, sequence, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: RecountDB has parent organization: National Institute of Advanced Industrial Science and Technology |
National Genome Research Network ; INTEuropean Union Systems Institute ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:21209072 PMID:20144198 PMID:20110255 DOI:10.1093/nar/gkq010 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151594, biotools:last, OMICS_15813 | https://bio.tools/last, https://sources.debian.org/src/last-align/ | SCR_006119 | 2026-08-06 09:26:31 | 397 | |||||
|
GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-08-06 09:26:43 | 348 | ||||
|
ClinVar Resource Report Resource Website 5000+ mentions |
ClinVar (RRID:SCR_006169) | ClinVar | storage service resource, service resource, data repository, data or information resource, database | Archive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard. | sequence variation, variation, phenotype, genetics, genetic variation, clinical, allele, aggregator, geneotype, gene, disease, clinical assertion, bio.tools |
is used by: NIF Data Federation is used by: MARRVEL is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: AutoGVP has parent organization: NCBI |
Free, Freely available | nlx_151671, r3d100013331, biotools:clinvar, OMICS_00262 | https://bio.tools/clinvar, https://doi.org/10.17616/R31NJMS3 | SCR_006169 | 2026-08-06 09:26:31 | 6595 | |||||||
|
Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/, https://bio.tools/g2d | SCR_008190 | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-08-06 09:27:06 | 2 | |||||
|
FragGeneScan Resource Report Resource Website 100+ mentions |
FragGeneScan (RRID:SCR_011929) | sequence analysis software, software resource, data analysis software, data processing software, software application | A software application for finding fragmented genes in short reads and may be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. | microbiome, sequence analysis, fragment, gene, short read, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Acknowledgement requested, Available for download | OMICS_01484, biotools:fraggenescan | http://omics.informatics.indiana.edu/FragGeneScan/, https://bio.tools/fraggenescan | SCR_011929 | 2026-08-06 09:27:51 | 183 | ||||||||
|
Vmatch Resource Report Resource Website 10+ mentions |
Vmatch (RRID:SCR_018968) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | 2026-08-06 09:29:25 | 35 | ||||||||
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LTR_FINDER_parallel Resource Report Resource Website 10+ mentions |
LTR_FINDER_parallel (RRID:SCR_018969) | data analysis software, software application, software resource, data processing software | Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. | Parallelization, rapid identification, retrotransposons identification, repetitive sequences, large genomes, long terminal repeat, retrotrnsposon, parallel operation, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF IOS 1740874; United States Department of Agriculture National Institute of Food ; Agriculture and AgBioResearch at Michigan State University |
PMID:31857828 | Free, Available for download, Freely available | biotools:LTR_FINDER_parallel | https://bio.tools/LTR_FINDER_parallel | SCR_018969 | 2026-08-06 09:29:30 | 14 | ||||||
|
metaXplor Resource Report Resource Website |
metaXplor (RRID:SCR_019025) | web application, data or information resource, software resource | Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures. | Data storage, metagenomics, data filtering, data sharing, data exploration, metagenomic data, viral data, microbial data, data manager, datasets sharing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Restricted | biotools:metaxplor | https://metaxplor.cirad.fr/metaXplor/, https://bio.tools/metaxplor | SCR_019025 | 2026-08-06 09:29:24 | 0 | ||||||||
|
GigaSOM.jl Resource Report Resource Website 1+ mentions |
GigaSOM.jl (RRID:SCR_019020) | data visualization software, software application, software resource, data processing software | Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets. | Flow cytometry data, flow cytometry data clustering, data clustering, data visualization, Julia, datasets, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/2020.08.03.234187 | Free, Available for download, Freely available | biotools:GigaSOM.jl | https://bio.tools/GigaSOM.jl | SCR_019020 | 2026-08-06 09:29:26 | 2 | |||||||
|
TRAL Resource Report Resource Website |
TRAL (RRID:SCR_018979) | TRAL | sequence analysis software, software resource, algorithm resource, data analysis software, data processing software, software application | Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions. | Annotation, tandem repeats annotation, amino acid repeats, nucleic data, statistical analysis, redundant predictions filtering, redundant annotation clustering, overlapping annotations clustering, false positive annotation filtering, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss State Secretariat for Education ; Research ; and Innovation |
DOI:10.1093/bioinformatics/btv306 | Free, Freely available | biotools:tral | https://bio.tools/tral | SCR_018979 | Tandem Repeat Annotation Library | 2026-08-06 09:29:30 | 0 | ||||
|
VICMpred Resource Report Resource Website 1+ mentions |
VICMpred (RRID:SCR_019039) | data access protocol, web service, software resource | Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule. | Bacterial protein, protein functional classification, virulence factor, metabolism molecule, information molecule, cellular process, gram negative bacteria, functional proteins prediction, amino acid patterns, aminoacid composition, dipeptide composition, bacterial protein sequences., bio.tools |
is listed by: Debian is listed by: bio.tools |
Council of Scientific and Industrial Research and Department of Biotechnology ; Government of India |
PMID:16689701 | Free, Freely available | biotools:vicmpred | https://bio.tools/vicmpred | SCR_019039 | Cellular process and Metabolism molecule in the bacterial proteins., Information molecule, Prediction of Virulence factors | 2026-08-06 09:29:26 | 2 | |||||
|
Annotree Resource Report Resource Website 10+ mentions |
Annotree (RRID:SCR_018980) | web service, data access protocol, data or information resource, software resource | Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes. | Genome annotation, genome visualization, phylogenetic tree, functionally annotated tree, microbial tree of life, taxonomic data, phylogenetic data, functionally annotated data, bacterial genome, archaeal genome, genome distribution, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Ontario Early Researcher award ; NSERC Discovery Grant ; Australian Research Council Laureate Fellowship ; Tier II Canada Research Chair ; Natural Sciences and Engineering Research Council of Canada |
PMID:31081040 | Free, Freely available | biotools:Annotree | https://bio.tools/AnnoTree | SCR_018980 | AnnoTree 1.2 | 2026-08-06 09:29:23 | 22 | |||||
|
Pyntacle Resource Report Resource Website 1+ mentions |
Pyntacle (RRID:SCR_019030) | software resource, network analysis software, data analysis software, data processing software, software application | Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools. | Graph analysis, topology, group centrality, systems biology, parallel computing, data conversion tool, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:pyntacle | https://bio.tools/pyntacle | SCR_019030 | 2026-08-06 09:29:30 | 1 | ||||||||
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StoatyDive Resource Report Resource Website 1+ mentions |
StoatyDive (RRID:SCR_018796) | data analysis software, software application, software resource, data processing software | Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data. | Evaluate predicted peak profile, classify predicted peak profile, assess binding specificity, protein-target specificity, sequencing data, CLIP-seq data, CHIP-Seq data, peak profile data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | SCR_018800, biotools:StoatyDive | https://bio.tools/StoatyDive | SCR_018796 | 2026-08-06 09:29:22 | 1 | ||||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, software application, software resource, data processing software | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-08-06 09:29:23 | 3 | ||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | software resource, data analysis software, data processing software, data visualization software, software application | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-08-06 09:29:30 | 1 | ||||||||
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Seqtk Resource Report Resource Website 500+ mentions |
Seqtk (RRID:SCR_018927) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software fast and lightweight tool for processing sequences in FASTA or FASTQ format. | Sequence processing, FASTA format, FASTQ format, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_09736, biotools:seqtk | https://bio.tools/seqtk, https://sources.debian.org/src/seqtk/ | SCR_018927 | SEQTK | 2026-08-06 09:29:23 | 827 | |||||||
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CopyDetective Resource Report Resource Website 1+ mentions |
CopyDetective (RRID:SCR_018909) | software resource, algorithm resource, data analysis software, data processing software, software application | Software tool for detection threshold aware CNV calling in matched whole exome sequencing data. | Copy number variant calling, whole exome sequencing data, detection thresholds, deletion, duplication, case control samples, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Munster; North Rhine-Westphalia; Germany |
EU 634789 (Horizon2020 MDS-RIGHT); DFG TU 298/5-1 (DFG Clinical Research Unit 326 Male Germ Cells: from Genes to Function); DKH 111347; Löwenkinder - Verein zur Unterstützung krebskranker Kinder e.V. ; DKS DKS349 2014.11 A/B (NHL-BFM Registry 2012) |
Free, Available for download, Freely available | biotools:copydetective | https://bio.tools/copydetective | SCR_018909 | 2026-08-06 09:29:24 | 1 | |||||||
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GEMB Resource Report Resource Website 1+ mentions |
GEMB (RRID:SCR_018904) | data analysis software, software application, software resource, data processing software | Software tool to introduce gene set enrichment for mathematical biology. Measures association between disease of interest and set of genes related to biological pathway. Used for defining gene contributions based on biophysical properties, by leveraging mathematical models of biology to predict effects of genetic perturbations on particular downstream function. | Gene set enrichement, mathematical biology, disease and gene association, biophysical property, gene perturbation prediction, weighted gene set test, recover p-value, bio.tools |
uses: MATLAB is listed by: bio.tools is listed by: Debian |
DOI:10.1101/554212 | Free, Freely available | biotools:gemb | https://bio.tools/gemb | SCR_018904 | Gene Set Enrichment for Mathematical Biology | 2026-08-06 09:29:29 | 1 |
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