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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | software application, data processing software, software toolkit, image analysis software, software resource, alignment software | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/ https://www.genome.jp/tools-bin/mafft https://myhits.isb-sib.ch/cgi-bin/mafft https://bio.tools/MAFFT https://sources.debian.org/src/mafft/ |
SCR_011811 | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-02-16 09:48:02 | 22450 | |||||
|
AdapterRemoval Resource Report Resource Website 500+ mentions |
AdapterRemoval (RRID:SCR_011834) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support. | cleaning of next-generation sequencing reads, remove residual adapter sequences, adapter, sequence, residual, next generation sequencing reads, |
is listed by: OMICtools is listed by: Debian |
Danish National Research Foundation ; Lundbeck Foundation Grant ; Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme ; Danish Council for Independent Research |
PMID:22748135 PMID:26868221 DOI:10.1186/s13104-016-1900-2 |
Free, Available for download, Freely available | OMICS_01081 | https://sources.debian.org/src/adapterremoval/ | http://code.google.com/p/adapterremoval/, https://github.com/slindgreen/AdapterRemoval, https://sources.debian.org/src/adapterremoval/ | SCR_011834 | AdapterRemoval v2 | 2026-02-16 09:48:00 | 675 | ||||
|
Axe Resource Report Resource Website 1+ mentions |
Axe (RRID:SCR_015984) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples. | software, tool, sequence, analysis, barcode, demultiplexing |
is listed by: Debian is listed by: OMICtools |
Free, Freely available, Available for download | OMICS_19788 | https://readthedocs.org/projects/axe-demultiplexer/ https://sources.debian.org/src/baitfisher/ |
SCR_015984 | Axe-demultiplexer | 2026-02-16 09:48:55 | 1 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | software application, data processing software, software toolkit, data analysis software, data management software, software resource | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools https://sources.debian.org/src/bamtools/ |
SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-02-16 09:48:55 | 324 | ||||||
|
G-Anchor Resource Report Resource Website 1+ mentions |
G-Anchor (RRID:SCR_016046) | G-Anchor | software application, data processing software, sequence analysis software, data analysis software, image analysis software, software resource, alignment software | Software for comparing large genomes and exploiting highly conserved sequences as evolutionary-stable "anchors". The pipeline maps a newly sequenced genome (assembled in scaffolds) on a reference genome without the need of a supercomputer. | anchor, comparison, scaffold, whole genome, alignment, sequence, mapping, anchoring, highly conserved elements, hce, evolution | HPC Wales ; Biotechnology and Biological Sciences Research Council BB/J010170/1 |
Free, Available for download | SCR_016046 | G-Anchor: A novel approach for cross-species comparison | 2026-02-16 09:48:59 | 1 | ||||||||
|
Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | software application, data processing software, image analysis software, software resource, alignment software | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Grant 098051; NHGRI U54 HG00455 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-02-16 09:48:55 | 2 | |||||||
|
HiLive Resource Report Resource Website |
HiLive (RRID:SCR_016134) | software application, data processing software, sequence analysis software, data analysis software, 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 | 2026-02-16 09:48:57 | 0 | |||||
|
FSA Resource Report Resource Website 1+ mentions |
FSA (RRID:SCR_016114) | FSA | software application, data processing software, image analysis software, software resource, alignment software | 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 | 2026-02-16 09:48:59 | 3 | ||||||
|
GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | software application, data processing software, data analysis software, 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 | 2026-02-16 09:48:57 | 279 | ||||||
|
DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | software application, data processing software, sequence analysis software, data analysis software, 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 | 2026-02-16 09:48:56 | 386 | |||||||
|
Glam2 Resource Report Resource Website 50+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | 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 | 2026-02-16 09:48:57 | 72 | |||||
|
E-mem Resource Report Resource Website 10+ mentions |
E-mem (RRID:SCR_016081) | E-mem | software application, data processing software, image analysis software, software resource, alignment software, 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 | 2026-02-16 09:48:57 | 12 | ||||
|
GenomeTools Resource Report Resource Website 100+ mentions |
GenomeTools (RRID:SCR_016120) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | 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 | 2026-02-16 09:48:57 | 131 | ||||||
|
Circlator Resource Report Resource Website 100+ mentions |
Circlator (RRID:SCR_016058) | software application, data processing software, software toolkit, image analysis software, software resource, alignment software | 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 | 2026-02-16 09:48:56 | 321 | ||||||
|
Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | software application, data processing software, data visualization software, 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 |
NIH P20 RR16448; INBRE Program of the National Center for Research Resources ; NSF EPS 00809035; NIH P20 RR16454 |
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 | 2026-02-16 09:48:56 | 26 | ||||||
|
MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | data repository, storage service resource, portal, service resource, data or information 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) |
the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the European Commission within the Research Infrastructures programme of Horizon 2020 676559; InnovateUK 102513; Research Councils UK (RCUK) ; EMBL ; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; EU Seventh Framework Programme for Research MICROB3 |
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 | 2026-02-16 09:49:01 | 51 | |||||
|
ASTRA Resource Report Resource Website 50+ mentions |
ASTRA (RRID:SCR_016255) | software application, data processing software, software toolkit, data analysis software, software resource | 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 | 2026-02-16 09:48:59 | 88 | |||||||||||
|
Entrez Resource Report Resource Website 10+ mentions |
Entrez (RRID:SCR_016640) | web service, data access protocol, software resource, portal, data or information resource | 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 | 2026-02-16 09:49:04 | 15 | ||||||||||
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MOLE-BLAST Resource Report Resource Website 1+ mentions |
MOLE-BLAST (RRID:SCR_016644) | moleblast, Mole Blast, MOLE BLAST | software application, data processing software, web service, sequence analysis software, data analysis software, data access protocol, software resource | 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 | 2026-02-16 09:49:04 | 1 | |||||||||
|
VecScreen Resource Report Resource Website 10+ mentions |
VecScreen (RRID:SCR_016577) | software application, data processing software, sequence analysis software, data analysis software, software resource, service resource | Software tool to screen a nucleic acid sequence for vector contamination. Detects foreign DNAs such as vector, linker, adapter, and primer regions involved in nucleotide sequences by using blast search against vector sequence database. The main unit of this tool is vecscreen program obtainable from NCBI. | screen, sequence, nucleic acid, segment, vector, contamination | is listed by: OMICtools | Free, Available for download, Freely available | https://www.ddbj.nig.ac.jp/vecscreen-help-e.html | SCR_016577 | 2026-02-16 09:49:03 | 48 |
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