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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Bioinformatics Toolkit Resource Report Resource Website 100+ mentions |
Bioinformatics Toolkit (RRID:SCR_010277) | software resource, software toolkit | A platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated. | bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1038/NMETH.1818 | nlx_156936, OMICS_28407, biotools:bioinformatics_toolkit | https://bio.tools/bioinformatics_toolkit, https://sources.debian.org/src/hhsuite/ | SCR_010277 | 2026-08-08 12:05:17 | 261 | ||||||||
|
VISTA Browser Resource Report Resource Website 100+ mentions |
VISTA Browser (RRID:SCR_011808) | software resource, software toolkit | Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. | Comparative genomics tools, genomic sequences, comparative analysis, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
Office of Biological and Environmental Research ; Office of Science ; US Department of Energy ; NHLBI |
PMID:15215394 | Free, Freely available | OMICS_00948, biotools:vista | http://genome.lbl.gov/vista/index.shtml, https://bio.tools/vista | SCR_011808 | VISTA, vista | 2026-08-08 12:05:19 | 125 | |||||
|
NSeq Resource Report Resource Website 10+ mentions |
NSeq (RRID:SCR_010891) | NSeq | software resource, software application | A multithreaded Java application for finding positioned nucleosomes from sequencing data. | is listed by: OMICtools | OMICS_00506 | SCR_010891 | 2026-08-08 12:05:14 | 12 | ||||||||||
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Bioinformatics.fr Resource Report Resource Website |
Bioinformatics.fr (RRID:SCR_011987) | Bioinformatics.fr | data or information resource, narrative resource | A web magazine helping bioinformatician or scientists find jobs, conferences, courses, companies and more stuff related to Bioinformatics. | bioinformatics | is listed by: OMICtools | OMICS_01728 | SCR_011987 | 2026-08-08 12:05:15 | 0 | |||||||||
|
BioCaster Resource Report Resource Website 1+ mentions |
BioCaster (RRID:SCR_011869) | BioCaster | software resource, service resource | Service that retrieves disease relevant information from Twitter tweets and shows current hotspots of disease outbreaks on an interactive map. It is an ontology-driven system for detecting global health events | outbreak, pathogen, geographical location, latitude, longitude, map, text-mining, public health, health hazard, monitoring, twitter, global |
is listed by: OMICtools has parent organization: National Institute of Informatics; Tokyo; Japan is parent organization of: BioCaster Ontology |
Infectious disease | Japan Science and Technology Agency ; Japan Society for the Promotion of Science ; ROIS Transdisciplinary Integration Project |
PMID:18922806 | GNU General Public License | OMICS_01174 | SCR_011869 | 2026-08-08 12:05:08 | 3 | |||||
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Eucalyptus Resource Report Resource Website 10+ mentions |
Eucalyptus (RRID:SCR_011872) | Eucalyptus | software resource, service resource | Open source software for building AWS-compatible private and hybrid clouds for IT organizations in enterprises and technology businesses. | cloud | is listed by: OMICtools | Open unspecified license | OMICS_01202 | SCR_011872 | Elastic Utility Computing Architecture for Linking Your Programs to Useful Systems | 2026-08-08 12:05:19 | 17 | |||||||
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PRESTO: Genetic Association Analysis Software Resource Report Resource Website 1+ mentions |
PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) | software resource, software application | Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data. | gene, genetic, genomic, java, ms-windows, unix, solaris, linux, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu138 | nlx_154549 | SCR_013285 | 2026-08-08 12:05:09 | 2 | |||||||||
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GoGrid Resource Report Resource Website |
GoGrid (RRID:SCR_013204) | GoGrid | software resource, service resource | Commercial software company offering on-demand cloud, hybrid hosting, hosted private cloud, and dedicated infrastructure for complex needs. | cloud, big data | is listed by: OMICtools | OMICS_01203 | SCR_013204 | 2026-08-08 12:05:20 | 0 | |||||||||
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THESIAS Resource Report Resource Website 50+ mentions |
THESIAS (RRID:SCR_013449) | THESIAS | software resource, software application | Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btm058 | nlx_154102, OMICS_19747, biotools:tHESIAS | https://bio.tools/THESIAS, https://sources.debian.org/src/thesias/ | http://ecgene.net/genecanvas/downloads.php?cat_id=1 | SCR_013449 | Testing Haplotype EffectS In Association Studies | 2026-08-08 12:05:10 | 53 | |||||
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PhyML Resource Report Resource Website 5000+ mentions |
PhyML (RRID:SCR_014629) | web application, software resource, source code | Web phylogeny server based on the maximum-likelihood principle. | phylogenic software, phylogeny, maximum likelihood, web server, bio.tools |
is used by: ProtTest is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: PAML |
DOI:10.1093/molbev/msq060 | Public server, Source code is available on request | biotools:phyml, OMICS_04241 | https://bio.tools/phyml, https://sources.debian.org/src/phyml/ | SCR_014629 | 2026-08-08 12:05:22 | 7951 | |||||||
|
MultiQC Resource Report Resource Website 1000+ mentions |
MultiQC (RRID:SCR_014982) | software resource, data access protocol | Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python. | bioinformatics, data aggregate, python, open source, html report, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Science for Life Laboratory ; National Genomics Infrastructure |
PMID:27312411 DOI:10.1093/bioinformatics/btw354 |
Open source, Available for download | biotools:multiqc, OMICS_12426 | https://github.com/ewels/MultiQC https://pypi.python.org/pypi/multiqc, https://bio.tools/multiqc, https://sources.debian.org/src/multiqc/ | SCR_014982 | 2026-08-08 12:05:14 | 3714 | ||||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-08-08 12:05:15 | 57 | |||||
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ABACAS Resource Report Resource Website 100+ mentions |
ABACAS (RRID:SCR_015852) | ABACAS | software resource, software application | Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account. | contiguation, primer, shotgun assembled contig, reference sequence, assembled sequence |
is listed by: Debian is listed by: OMICtools |
European Union LSHP-LT-2004-503578; Wellcome Trust Sanger Institute |
Free, Available for download | OMICS_06933 | https://sourceforge.net/projects/abacas/files/, https://sources.debian.org/src/abacas/ | SCR_015852 | ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences, Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS), Algorithm Based Automatic Contiguation of Assembled Sequences | 2026-08-08 12:05:15 | 178 | |||||
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Ecopcr Resource Report Resource Website 10+ mentions |
Ecopcr (RRID:SCR_016082) | Ecopcr | software resource, software application | Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | electronic, PCR, estimate, primers, quality, barcode |
is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_19861 | https://sources.debian.org/src/ecopcr/ | http://www.grenoble.prabi.fr/trac/ecoPCR/ | SCR_016082 | Ecopcr: Electronic polymerase chain reaction | 2026-08-08 12:05:20 | 27 | |||||
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Concavity Resource Report Resource Website 50+ mentions |
Concavity (RRID:SCR_016063) | software toolkit, software resource, software application | Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets. | predict, protein, ligand, binding, site, catalytic, drug, algorithm |
is listed by: Debian is listed by: OMICtools is related to: Princeton University; New Jersey; USA |
PMID:19997483 DOI:10.1371/journal.pcbi.1000585 |
Free, Available for download | OMICS_04161 | http://manpages.ubuntu.com/manpages/bionic/man1/concavity.1.html, https://sources.debian.org/src/concavity/ | SCR_016063 | 2026-08-08 12:05:24 | 94 | |||||||
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Mash Resource Report Resource Website 50+ mentions |
Mash (RRID:SCR_019135) | software resource, data analytics software, software application | Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. | Genome distance estimation, metagenome distance estimation, MinHash, mutation distance, sequence, sequence set |
is listed by: Debian is listed by: OMICtools |
NHGRI ; NIH |
PMID:27323842 | Free, Available for download, Freely available | OMICS_10468 | https://mash.readthedocs.io/en/latest/, https://sources.debian.org/src/mash/ | SCR_019135 | 2026-08-08 12:05:25 | 75 | ||||||
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Scoary Resource Report Resource Website 10+ mentions |
Scoary (RRID:SCR_021087) | software resource, data analytics software, software application | Software tool that scores components of pan genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.Designed to take gene presence absence.csv file from Roary as well as traits file created by user and calculate associations between all genes in accessory genome and traits. It reports list of genes sorted by strength of association per trait. | Gene associations calculation, accessory genome, phenotypic traits, gene presence, gene absence, gene sort, association strenght |
is listed by: Debian is listed by: OMICtools works with: Roary |
Norwegian Institute of Public Health ; Norwegian Research Council |
PMID:27887642 | Free, Available for download, Freely available | OMICS_13120 | https://sources.debian.org/src/scoary/ | SCR_021087 | 2026-08-08 12:05:26 | 20 | ||||||
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EpiFactors Resource Report Resource Website 10+ mentions |
EpiFactors (RRID:SCR_016956) | database, data or information resource | Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products. | manually, curated, collection, human, epigenetic, factor, complex, corresponding, gene, target, product | is listed by: OMICtools | Russian Fund For Basic Research ; Ministerio de Economia Y Competividad ; Spain ; Åke Olsson’s foundation ; Swedish Cancer foundation ; Swedish Childhood cancer foundation ; Dynasty Foundation Fellowship ; Japanese Ministry of Education ; Culture ; Sports ; Science and Technology ; Norwegian University of Science and Technology |
PMID:26153137 | Free, Available for download, Freely available | SCR_016956 | 2026-08-08 12:04:40 | 24 | ||||||||
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miRTarBase Resource Report Resource Website 100+ mentions |
miRTarBase (RRID:SCR_017355) | database, data or information resource | Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs. | Manually, curated, experimentally, validated, database, microRNA, target, interaction, collection, data, MTI, FASEB list | is listed by: OMICtools | Ministry of Science and Technology ; Taiwan |
PMID:29126174 | Free, Available for download, Freely availabe | http://mirtarbase.mbc.nctu.edu.tw/php/index.php | SCR_017355 | microRNA-Target interactions Base | 2026-08-08 12:04:34 | 432 | ||||||
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Geno2MP Resource Report Resource Website 1+ mentions |
Geno2MP (RRID:SCR_016872) | Geno2MP | database, data or information resource, service resource | Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community. | data, collection, Mendelian, phenotype, affected, individuals, profile, human, genetics |
is used by: MARRVEL is listed by: OMICtools |
University of Washington Center for Mendelian Genomics ; Seattle ; WA |
Free, Available for download, Freely available | SCR_016872 | Geno2MP, 2 Mendelian Phenotype, The Genotype 2 Mendelian Phenotype database | 2026-08-08 12:04:34 | 2 |
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