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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 | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | 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 | 2026-09-19 12:52:18 | 24687 | |||||
|
CGView Resource Report Resource Website 100+ mentions |
CGView (RRID:SCR_011779) | CGView | software resource | A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Alberta; Alberta; Canada |
DOI:10.1093/bioinformatics/bti054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00905, biotools:cgview | https://bio.tools/cgview, https://sources.debian.org/src/cgview/ | SCR_011779 | Circular Genome Viewer | 2026-09-19 12:52:18 | 310 | |||||
|
PSAR-Align Resource Report Resource Website 1+ mentions |
PSAR-Align (RRID:SCR_011814) | PSAR-Align | software resource | Software for improving multiple sequence alignment using probabilistic sampling. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24222208 | Free | OMICS_00987, biotools:psar | https://bio.tools/psar | SCR_011814 | PSAR-Align: improving multiple sequence alignment using probabilistic sampling | 2026-09-19 12:52:18 | 1 | |||||
|
Gaggle Resource Report Resource Website |
Gaggle (RRID:SCR_011780) | Gaggle | software resource | An open source software tool for visualizing high-density data plotted against coordinates on the genome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Open unspecified license, Free | biotools:ggb, OMICS_00909 | https://bio.tools/ggb | SCR_011780 | 2026-09-19 12:52:18 | 0 | |||||||
|
HiTEC Resource Report Resource Website 1+ mentions |
HiTEC (RRID:SCR_011826) | HiTEC | software resource | Accurate error correction in high-throughput sequencing data. | is listed by: OMICtools | OMICS_01105 | SCR_011826 | 2026-09-19 12:52:19 | 6 | ||||||||||
|
PatMaN Resource Report Resource Website 50+ mentions |
PatMaN (RRID:SCR_011821) | PatMaN | software resource | Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18467344 DOI:10.1093/bioinformatics/btn223 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00997, biotools:patman | https://bio.tools/patman, https://sources.debian.org/src/patman/ | SCR_011821 | PatMaN - A DNA pattern matcher for short sequences | 2026-09-19 12:52:19 | 61 | |||||
|
Hammer Resource Report Resource Website 100+ mentions |
Hammer (RRID:SCR_011825) | Hammer | software resource | A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of California at San Diego; California; USA |
PMID:21685062 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01103 | SCR_011825 | Hammer: error correction with non-uniform coverage | 2026-09-19 12:52:19 | 196 | |||||||
|
Genome Projector Resource Report Resource Website 1+ mentions |
Genome Projector (RRID:SCR_011790) | Genome Projector | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource | A searchable database browser with zoomable user interface using Google Map API. Genome Projector currently contains 4 views: Genome map, Plasmid map, Pathway map, and DNA walk. | genome, plasmid, pathway, dna, map, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Japan Society for the Promotion of Science | GNU General Public License, V.2 | OMICS_00912, biotools:genome_projector | https://bio.tools/genome_projector | SCR_011790 | 2026-09-19 12:52:18 | 3 | ||||||
|
GNomEx Resource Report Resource Website 1+ mentions |
GNomEx (RRID:SCR_011805) | GNomEx | data repository, service resource, storage service resource | A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets. |
is listed by: OMICtools has parent organization: University of Utah; Utah; USA |
PMID:20828407 | OMICS_01005 | https://uofuhealth.utah.edu/huntsman/shared-resources/gba/bioinformatics/software/ | http://hci-scrum.hci.utah.edu/gnomexdoc/ | SCR_011805 | 2026-09-19 12:52:18 | 5 | |||||||
|
Infernal Resource Report Resource Website 500+ mentions |
Infernal (RRID:SCR_011809) | Infernal | software resource | Software for searching DNA sequence databases for RNA structure and sequence similarities. | FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: ANNOgesic has parent organization: Janelia Research |
PMID:24008419 DOI:10.1093/bioinformatics/btp157 |
GNU General Public License, v3 | OMICS_00977 | https://sources.debian.org/src/infernal/ | SCR_011809 | Infernal: inference of RNA alignments, INFERence of RNA Alignment | 2026-09-19 12:52:18 | 772 | |||||
|
GenomeMatcher Resource Report Resource Website 50+ mentions |
GenomeMatcher (RRID:SCR_011800) | GenomeMatcher | software resource | A graphical interface for comparative genomics. | is listed by: OMICtools | OMICS_00936 | SCR_011800 | 2026-09-19 12:52:18 | 65 | ||||||||||
|
GenomeRing Resource Report Resource Website 1+ mentions |
GenomeRing (RRID:SCR_011801) | GenomeRing | software resource | Alignment visualization based on SuperGenome coordinates. |
is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
OMICS_00937 | SCR_011801 | 2026-09-19 12:52:18 | 2 | ||||||||||
|
Gobe Resource Report Resource Website 1+ mentions |
Gobe (RRID:SCR_011802) | Gobe | software resource | An interactive, web-based tool for comparative genomic visualization. | is listed by: OMICtools | OMICS_00938 | SCR_011802 | 2026-09-19 12:52:18 | 2 | ||||||||||
|
GSV Resource Report Resource Website 1+ mentions |
GSV (RRID:SCR_011803) | GSV | software resource | Software that allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them. | is listed by: OMICtools | OMICS_00939 | SCR_011803 | Genome Synteny Viewer | 2026-09-19 12:52:18 | 2 | |||||||||
|
NextGENe Resource Report Resource Website 100+ mentions |
NextGENe (RRID:SCR_011859) | NextGENe | data analysis software, data processing software, software application, software resource | Software tool for Next Generation sequence analysis. Analytical partner for analysis of desktop sequencing data produced by Illumina iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. Software runs on Windows Operating System, which provides biologist friendly interface. It does not require scripting or other bioinformatics support. | Next Generation Sequence Analysis, desktop sequencing data analysis, sequencing data | is listed by: OMICtools | Commercial license | OMICS_01131 | http://softgenetics.com/NextGENe.html | SCR_011859 | Next GENeration Sequence Analysis | 2026-09-19 12:52:19 | 381 | ||||||
|
RACER Resource Report Resource Website 10+ mentions |
RACER (RRID:SCR_011852) | RACER | software resource | A software program for correcting errors in sequencing data. | is listed by: OMICtools | OMICS_01108 | SCR_011852 | 2026-09-19 12:52:19 | 37 | ||||||||||
|
NARWHAL Resource Report Resource Website 10+ mentions |
NARWHAL (RRID:SCR_011858) | NARWHAL | software resource | Automates the primary analysis of massive parallel sequencing data. |
is listed by: OMICtools has parent organization: Netherlands Bioinformatics Centre |
OMICS_01130 | SCR_011858 | 2026-09-19 12:52:19 | 10 | ||||||||||
|
UTGB Toolkit Resource Report Resource Website 1+ mentions |
UTGB Toolkit (RRID:SCR_011797) | UTGB Toolkit | software resource | An open-source software for developing personalized genome browsers that work in web browsers. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
Open unspecified license | OMICS_00927, biotools:utgb_toolkit | https://bio.tools/utgb_toolkit | SCR_011797 | University of Tokyo Genome Browser | 2026-09-19 12:52:18 | 1 | ||||||
|
AdapterRemoval Resource Report Resource Website 500+ mentions |
AdapterRemoval (RRID:SCR_011834) | data analysis software, data processing software, sequence analysis software, software application, 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 Council for Independent Research ; Danish National Research Foundation ; Lundbeck Foundation Grant ; Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme |
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 | 2026-09-19 12:52:19 | 773 | ||||
|
Btrim Resource Report Resource Website 50+ mentions |
Btrim (RRID:SCR_011836) | Btrim | software resource | A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:21651976 | biotools:btrim, OMICS_01083 | https://bio.tools/btrim | SCR_011836 | 2026-09-19 12:52:19 | 87 |
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