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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Aragorn Resource Report Resource Website 100+ mentions |
Aragorn (RRID:SCR_015974) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that detects tRNA genes and tmRNA genes in nucleotide sequences. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base‐paired cloverleaf., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | software, program, nucleotide, sequence, detect, tmRNA, tRNA |
is listed by: Debian is listed by: OMICtools |
PMID:14704338 DOI:10.1093/nar/gkh152 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04227 | https://sources.debian.org/src/arden/ | SCR_015974 | 2026-09-03 04:53:22 | 474 | |||||||
|
DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-09-03 04:53:46 | 489 | |||||||
|
Circlator Resource Report Resource Website 100+ mentions |
Circlator (RRID:SCR_016058) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes. | assembly, sequence, genome, DNA, circularization, accurate, bacteria, erukaryote, tool |
is listed by: Debian is listed by: OMICtools |
Wellcome Trust grant 098051 | PMID:26714481 DOI:10.1186/s13059-015-0849-0 |
Free, Available for download | OMICS_09488 | https://github.com/sanger-pathogens/circlator, https://sources.debian.org/src/circlator/ | SCR_016058 | 2026-09-03 04:53:21 | 363 | ||||||
|
Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | data processing software, data visualization software, software application, software resource, standalone software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rnj, phylogenetic, tree, construction, neighbor, joining, distance, method, reference, standalone, implemetation, relaxed, algorithm, phylogenetic, tree, reconstruction, sequence |
is listed by: Debian is listed by: OMICtools is related to: University of Idaho; Idaho; USA |
INBRE Program of the National Center for Research Resources ; NIH P20 RR16448; NIH P20 RR16454; NSF EPS 00809035 |
PMID:16752216 DOI:10.1007/s00239-005-0176-2 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15083 | https://github.com/ibest/clearcut, https://sources.debian.org/src/clearcut/ | SCR_016059 | 2026-09-03 04:53:32 | 26 | ||||||
|
ASTRA Resource Report Resource Website 50+ mentions |
ASTRA (RRID:SCR_016255) | data analysis software, data processing software, software application, software resource, software toolkit | Software for the characterization of macromolecules and nanoparticles via multi-angle and dynamic light scattering. It simplifies MALS and DLS analysis for assessment of molar mass, size, conformation, conjugation, and other essential physical parameters. | macromolecule, nanoparticle, light, scattering, mals, dls, hplc, sequence, processing | SCR_016255 | ASTRA6, Wyatt Technologies ASTRA, ASTRA Software | 2026-09-03 04:53:51 | 92 | |||||||||||
|
HiLive Resource Report Resource Website |
HiLive (RRID:SCR_016134) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications. | perform, read, mapping, sequence, alignment, analysis, Illumina, time, critical, clinical, application |
is listed by: Debian is listed by: OMICtools |
the German Federal Ministry of Health IIA5-2512-FSB-725 | PMID:27794555 | Free, Available for download | OMICS_13393 | https://sources.debian.org/src/hilive/ | https://sourceforge.net/projects/hilive/ | SCR_016134 | 2026-09-03 04:53:35 | 0 | |||||
|
FSA Resource Report Resource Website 1+ mentions |
FSA (RRID:SCR_016114) | FSA | alignment software, data processing software, image analysis software, software application, software resource | Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned. | multiple, sequence, alignment, algorithm, distance, approach, homologous, protein, DNA, RNA, acurate, fast |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:19478997 | Free, available for download | https://sources.debian.org/src/fsa/ | SCR_016114 | Fast Statistical Alignment, FSA: Fast Statistical Alignment | 2026-09-03 04:53:24 | 3 | ||||||
|
GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | data analysis software, data processing software, software application, software resource | Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution. | inference, phylogenetic, tree, analysis, molecular, sequence, data, maximum, likelihood, criterion, nucleotide, amino acid, codon, model, evolution |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_04234 | https://code.google.com/archive/p/garli/, https://sources.debian.org/src/garli/ | SCR_016117 | Genetic Algorithm for Rapid Likelihood Inference | 2026-09-03 04:53:47 | 280 | ||||||
|
Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data analysis software, data processing software, software application, software resource | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-09-03 04:53:27 | 19 | |||||||
|
Glam2 Resource Report Resource Website 100+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets. | motif, analysis, sequence, find, amino acid, nucleotide, set, alignment, gapped, recurring, variable, letnght, pattern, DNA, protein, output, discovery, dataset | is related to: MEME Suite - Motif-based sequence analysis tools | NIGMS R01 GM103544 | PMID:18437229 | Free, Freely available for non-commercial use | http://meme-suite.org/ | SCR_016129 | Glam2: Gapped local alignment of motifs 2 | 2026-09-03 04:53:28 | 203 | |||||
|
E-mem Resource Report Resource Website 10+ mentions |
E-mem (RRID:SCR_016081) | E-mem | alignment software, data processing software, image analysis software, software application, software resource, standalone software | Software for an efficient maximal exact match (MEM) computation program that does not use full text indexes, uses less space and is amenable to parallelization. It can be used as a stand alone application or a drop-in replacement for MUMmer3 system for rapidly aligning entire genomes. | efficient, maximal, exact, match, compute, program, algorithm, application, sequence, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Department of Computer Science; University of Western Ontario; London; Ontario; Canada |
Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant R3143A01 (L.I.). | PMID:25399029 | Free, Available for download | OMICS_08451 | https://github.com/lucian-ilie/E-MEM, https://sources.debian.org/src/e-mem/ | SCR_016081 | E-mem: Efficient-maximal exact match | 2026-09-03 04:53:33 | 12 | ||||
|
GenomeTools Resource Report Resource Website 100+ mentions |
GenomeTools (RRID:SCR_016120) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization. | analysis, genome, annotate, sequence, compress, visualization, single, binary, combine, structure, efficient |
is listed by: Debian is listed by: OMICtools |
PMID:24091398 | Free, Available for download | OMICS_16119 | https://sources.debian.org/src/genometools/ | SCR_016120 | GenomeTool, Genome Tools, Genome Tool | 2026-09-03 04:53:28 | 150 | ||||||
|
Hyphygui Resource Report Resource Website 50+ mentions |
Hyphygui (RRID:SCR_016271) | data processing software, software application, data analysis software, software resource | It is an open-source software package for comparative sequence analysis using stochastic evolutionary models. Used for the analysis of genetic sequence data (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. | analysis, genetic, sequence, data, natural, selection, phylogenetic, molecular, evolution, machine, learning | MIDAS ; NIGMS R01 GM093939 |
Free, Available for download | SCR_016271 | HyPhy:Hypothesis Testing using Phylogenies | 2026-09-03 04:53:29 | 54 | |||||||||
|
MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | data or information resource, data repository, portal, service resource, storage service resource | Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020. | analysis, exploration, metagenomic, metatranscriptomic, amplicon, assembly, data, sequence, ENA, microbial, population, environment, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Debian is listed by: bio.tools is related to: NIDDK Information Network (dkNET) |
EMBL ; EU Seventh Framework Programme for Research MICROB3; InnovateUK 102513; Research Councils UK (RCUK) ; the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; the European Commission within the Research Infrastructures programme of Horizon 2020 676559 |
PMID:31696235 | Free, Freely available, Training online available | r3d100011192, biotools:MGnify | https://bio.tools/MGnify, https://doi.org/10.17616/R34W68 | SCR_016429 | , MGnify, EBI Metagenomics | 2026-09-03 04:53:36 | 74 | |||||
|
Portcullis Resource Report Resource Website 10+ mentions |
Portcullis (RRID:SCR_016442) | data analysis software, data processing software, software application, software resource | Software for filtering invalid Splice junctions from pre-aligned RNA-seq data. It takes as input a BAM file generated by an RNAseq mapper, then analyses and quantifies all splice junctions in the file before filtering (culling) those which are unlikely to be genuine. | filter, invalid, splicing, rnaseq, sequence, sequencing, bam, junction, rna | is related to: Mikado | Biotechnology and Biological Sciences Research Council (BBSRC) | Free, Available for download | SCR_016442 | 2026-09-03 04:53:41 | 33 | |||||||||
|
MAxEntScan Resource Report Resource Website 50+ mentions |
MAxEntScan (RRID:SCR_016707) | MAxEntScan | service resource, simulation software, software application, software resource | Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing. | modeling, sequence, short, motif, maximum, entropy, principle, MEP, RNA, splicing |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Lee Kuan Yew Scholarship for the goverment of Singapore ; NIH ; NSF Grant 0218506 |
PMID:15285897 | Free, Available for download, Freely available | SCR_016707 | Maximum Entropy Scan, MAxEntScan, MAximumEntropyScan | 2026-09-03 04:53:59 | 70 | ||||||
|
rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | data analysis software, data processing software, software application, software resource | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-09-03 04:53:54 | 1 | |||||||||
|
Entrez Resource Report Resource Website 10+ mentions |
Entrez (RRID:SCR_016640) | data access protocol, data or information resource, portal, software resource, web service | Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ. | global, query, cross, database, search, retrival, system, database, nucleotide, protein, sequence, data, genomic, mapping, structure, reference |
is affiliated with: PubChem BioAssay is related to: National Library of Medicine has parent organization: NCBI works with: Batch Entrez works with: Biotite |
Free, Freely available | SCR_016640 | 2026-09-03 04:53:47 | 17 | ||||||||||
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MOLE-BLAST Resource Report Resource Website 1+ mentions |
MOLE-BLAST (RRID:SCR_016644) | moleblast, Mole Blast, MOLE BLAST | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Software tool that helps taxonomists find closest database neighbors of submitted query sequences by generating a phylogenetic tree from BLAST results. | taxonomist, find, close, database, submitted, query, sequence, generate, phylogenetic, tree, nucleotide | works with: NCBI BLAST | Free, Freely available | SCR_016644 | 2026-09-03 04:54:08 | 3 | |||||||||
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Clonotator Resource Report Resource Website |
Clonotator (RRID:SCR_016730) | alignment software, data access protocol, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource, web service | Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data. | screening, annotation, cDNA, sequence, amino acid, align, reference, database, protein, disease, mutation, transcriptomic, data | has parent organization: University of California at San Francisco; California; USA | Free, Freely available, Registration required | https://willseylab.com/clonotator/ | SCR_016730 | 2026-09-03 04:54:00 | 0 |
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