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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Toolbox at the European Bioinformatics Institute Resource Report Resource Website 50+ mentions |
Toolbox at the European Bioinformatics Institute (RRID:SCR_002872) | software resource, software toolkit | The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI. | expression, functional, gene, bioinformatics, database, genomic, homology, protein, proteomic, sequence, structural, toolbox | has parent organization: European Bioinformatics Institute | Free | nif-0000-25553 | SCR_002872 | EBI Bioinformatics Tools | 2026-09-12 01:02:29 | 92 | ||||||||
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GS-EM Resource Report Resource Website |
GS-EM (RRID:SCR_003992) | GS-EM | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154366 | SCR_003992 | GenoSpectrum Expectation-Maximuzation | 2026-09-12 01:02:32 | 0 | ||||||||
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IBDREG Resource Report Resource Website |
IBDREG (RRID:SCR_013127) | software application, software resource | Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/s-plus | is listed by: Genetic Analysis Software | nlx_154588, SCR_009366, nlx_154407 | http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm | SCR_013127 | R/IBDREG | 2026-09-12 01:01:01 | 0 | ||||||||
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NeLS Resource Report Resource Website 1+ mentions |
NeLS (RRID:SCR_016301) | NeLS | data or information resource, organization portal, portal | Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project. | genomic, data, analyze, store, share, archive, electronic, infrastructure, administration, Norway, bio.tools |
is listed by: bio.tools is listed by: Debian |
Research Council of Norway | Free, Freely available | biotools:nels | https://bio.tools/nels, https://github.com/elixir-no-nels/nels-core, https://bio.tools/nels | SCR_016301 | Norwegian e-Infrastructure for Life Sciences | 2026-09-12 01:01:04 | 3 | |||||
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Mnemiopsis Genome Project Portal Resource Report Resource Website |
Mnemiopsis Genome Project Portal (RRID:SCR_018293) | MGP Portal | data or information resource, portal, project portal | Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis. | Genomic, data, metazoan development, Mnemiopsis leidyi, Ctenophore, moel organisms, genomic data analysis |
is related to: University of Michigan; Ann Arbor; USA is related to: Brown University; Rhode Island; USA is related to: University of Florida; Florida; USA |
Free, Freely available | SCR_018293 | 2026-09-12 01:01:07 | 0 | |||||||||
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Harvest-tools Resource Report Resource Website 1+ mentions |
Harvest-tools (RRID:SCR_016132) | software resource, software toolkit | Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. | archiving, postprocessing, reference, compressed, genomic, multialignment, create, interface, Gingr, file, phylogentic, tree, annotation, bioinformatic, format |
is listed by: Debian is listed by: OMICtools |
Department of Homeland Security Science and Technology Directorate | PMID:25410596 | Free, Available for download, Freely available | OMICS_08468 | https://github.com/marbl/harvest-tools, https://sources.debian.org/src/harvest-tools/ | SCR_016132 | 2026-09-12 01:02:53 | 4 | ||||||
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ENTROPY BLOCKER Resource Report Resource Website |
ENTROPY BLOCKER (RRID:SCR_000123) | ENTROPY BLOCKER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154300, nlx_154581, SCR_007247 | SCR_000123 | R/ENTROPY BLOCKER, R/ENTROPY_BLOCKER | 2026-09-12 01:01:18 | 0 | |||||||
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dbSTS Resource Report Resource Website 1+ mentions |
dbSTS (RRID:SCR_000400) | dbSTS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences. | genomic, mapping, sequence, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NIH | PMID:2781285 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dbsts, nif-0000-20939, r3d100010649 | https://bio.tools/dbsts, https://doi.org/10.17616/R39P5C | SCR_000400 | NCBI dbSTS: database of Sequence Tagged Sites, Sequence Tagged Sites Database, NCBI dbSTS, dbSTS: database of Sequence Tagged Sites, Database of Sequence Tagged Sites | 2026-09-12 01:01:19 | 3 | ||||
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ACGT Inc. Resource Report Resource Website |
ACGT Inc. (RRID:SCR_001026) | ACGT | analysis service resource, production service resource, service resource | Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels. | commercial, molecular biology, bioinformatics, genomic, service, dna sequencing | is listed by: ScienceExchange | Restricted | SciEx_10623 | http://www.scienceexchange.com/facilities/acgt-inc | SCR_001026 | 2026-09-12 01:01:21 | 0 | |||||||
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HOMOZYGOSITYMAPPER Resource Report Resource Website 100+ mentions |
HOMOZYGOSITYMAPPER (RRID:SCR_001714) | HomozygosityMapper | analysis service resource, data analysis service, production service resource, service resource | A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:19465395 | Free, Freely Available | nlx_154069, biotools:homozygositymapper, OMICS_00123 | https://bio.tools/homozygositymapper | SCR_001714 | 2026-09-12 01:01:23 | 125 | ||||||
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MADELINE Resource Report Resource Website 1+ mentions |
MADELINE (RRID:SCR_001979) | MADELINE | service resource, software application, software resource | Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. | gene, genetic, genomic, c, unix, solaris, freebsd, openbsd, macos, ms-windows, cygwin, linux, pedigree, draw, linkage association, family association |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:17488757 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154446, OMICS_00210 | http://eyegene.ophthy.med.umich.edu/#madeline | SCR_001979 | Madeline | 2026-09-12 01:01:23 | 5 | |||||
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Platypus Resource Report Resource Website 100+ mentions |
Platypus (RRID:SCR_005389) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data. | Haplotype based variant caller, next generation sequence data, gene, genomic, high throughput sequencing data, |
is listed by: OMICtools is related to: SAMTOOLS has parent organization: Wellcome Trust Centre for Human Genetics |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_009046, nlx_154021, OMICS_00068 | SCR_005389 | Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data, PLAYPUS | 2026-09-12 01:02:34 | 200 | ||||||||
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TDTPOWER Resource Report Resource Website |
TDTPOWER (RRID:SCR_005021) | TDTPOWER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software) | gene, genetic, genomic, sas macro | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154678 | SCR_005021 | 2026-09-12 01:02:34 | 0 | ||||||||
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POPDIST Resource Report Resource Website |
POPDIST (RRID:SCR_004904) | POPDIST | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, (aix/irix/decalpha), linux, macos, ms-dos, ms-windows, (95) | is listed by: Genetic Analysis Software | PMID:21564908 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154542 | SCR_004904 | 2026-09-12 01:02:34 | 0 | |||||||
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HAPLOCLUSTERS Resource Report Resource Website |
HAPLOCLUSTERS (RRID:SCR_007439) | HAPLOCLUSTERS | software application, software resource | Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
Aging | nlx_154014, biotools:haploclusters | https://bio.tools/haploclusters | SCR_007439 | 2026-09-12 01:02:37 | 0 | |||||||
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LDSUPPORT Resource Report Resource Website |
LDSUPPORT (RRID:SCR_007036) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, linux | is listed by: Genetic Analysis Software | nlx_154427 | SCR_007036 | 2026-09-12 01:02:36 | 0 | ||||||||||
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BETA Resource Report Resource Website 100+ mentions |
BETA (RRID:SCR_007556) | BETA | software application, software resource | Software application for non-parametric linkage analysis using allele sharing in sib pairs (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, sun | is listed by: Genetic Analysis Software | nlx_154241 | SCR_007556 | 2026-09-12 01:02:37 | 138 | |||||||||
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MAPCREATOR Resource Report Resource Website 1+ mentions |
MAPCREATOR (RRID:SCR_008001) | MAPCREATOR | software application, software resource | Software application to create gene maps using either radiation hybrid data or linkage data (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | nlx_154455 | SCR_008001 | 2026-09-12 01:02:37 | 4 | |||||||||
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Graphical Overview of Linkage Disequilibrium Resource Report Resource Website 1000+ mentions |
Graphical Overview of Linkage Disequilibrium (RRID:SCR_007151) | GOLD | software application, software resource | Software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data. | gene, genetic, genomic |
is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:10842743 | nlx_154363 | SCR_007151 | 2026-09-12 01:02:36 | 2212 | ||||||||
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PubMatrix Resource Report Resource Website 10+ mentions |
PubMatrix (RRID:SCR_008236) | software application, software resource, text-mining software | PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence. PubMatrix is a simple way to rapidly and systematically compare any list of terms against any other list of terms in PubMed. It reports back the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table. Lists of terms can be anything; gene names, diseases, gene functions, authors, etc. The user can then quickly sort or browse the frequency matrix table to do individual searches independently. This allows the user to build up tables of word relationships in PubMed in the context of your experiments or your scientific interests. This is useful for analyzing combinatorial datasets, as found with multiplex experimental systems, such as cDNA microarrays, genomic, proteomic, or other multiplex comparisons. The PubMatrix database is an archive of previous searches on many topics. Sponsors: PubMatrix is supported by the National Institutes of Health. | experiment, function, gene, author, cdna, combinatorial, comparison, dataset, disease, genomic, keyword, literature, matrix, medline interfaces, microarray, ncbi, proteomic, pubmed, scientific, system, term, text mining, FASEB list | has parent organization: National Institutes of Health | nif-0000-21348 | SCR_008236 | PubMatrix | 2026-09-12 01:02:37 | 35 |
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