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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MuSiC Resource Report Resource Website 100+ mentions |
MuSiC (RRID:SCR_008792) | MuSiC | software resource | A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., 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 has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22759861 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:MuSiC2, OMICS_00152 | https://bio.tools/MuSiC2 https://github.com/ding-lab/MuSiC2/blob/master/README.md |
SCR_008792 | Mutational Significance In Cancer | 2026-02-14 02:01:45 | 485 | |||||
|
GEMINI Resource Report Resource Website 500+ mentions |
GEMINI (RRID:SCR_014819) | software resource | Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD. | framework, genetic variation, annotation, human, genome, vcf, database, , bio.tools, FASEB list |
uses: KEGG uses: ENCODE uses: OMIM uses: dbSNP uses: HPRD - Human Protein Reference Database is listed by: Debian is listed by: bio.tools has parent organization: University of Utah; Utah; USA |
DOI:10.1371/journal.pcbi.1003153 | Freely available | biotools:gemini | https://github.com/arq5x/gemini https://bio.tools/gemini |
SCR_014819 | GEnome MINIng (GEMINI), GEMINI - a flexible framework for exploring genome variation, Genome Mining, GEnome MINIng | 2026-02-14 02:03:02 | 515 | ||||||
|
eDMR Resource Report Resource Website 10+ mentions |
eDMR (RRID:SCR_006960) | eDMR | software resource | Comprehensive differentially methylated regions (DMR) analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
MIT License | biotools:edmr, OMICS_00622 | https://bio.tools/edmr | SCR_006960 | 2026-02-14 02:01:26 | 19 | |||||||
|
Peakzilla Resource Report Resource Website 1+ mentions |
Peakzilla (RRID:SCR_007471) | Peakzilla | software resource | An algorithm to identify transcription factor binding sites from ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:peakzilla, OMICS_00454 | https://bio.tools/peakzilla | SCR_007471 | 2026-02-14 02:01:33 | 6 | ||||||||
|
AmpliconNoise Resource Report Resource Website 50+ mentions |
AmpliconNoise (RRID:SCR_007814) | AmpliconNoise | software resource | A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
DOI:10.1186/1471-2105-12-38 | biotools:pyronoise, OMICS_01112 | https://bio.tools/pyronoise https://sources.debian.org/src/anfo/ |
SCR_007814 | 2026-02-14 02:01:30 | 90 | |||||||
|
Kalign Resource Report Resource Website 100+ mentions |
Kalign (RRID:SCR_011810) | Kalign | software resource | A fast and accurate multiple sequence alignment algorithm. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:16343337 DOI:10.1093/bioinformatics/btz795 |
Free | OMICS_00978, biotools:kalign | https://bio.tools/kalign https://sources.debian.org/src/kalign/ |
SCR_011810 | 2026-02-14 02:02:27 | 119 | ||||||
|
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 | 2026-02-14 02:02:04 | 304 | |||||
|
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 | 2026-02-14 02:02:28 | 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 | 2026-02-14 02:02:26 | 0 | |||||||
|
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 | 2026-02-14 02:02:28 | 61 | |||||
|
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 | 2026-02-14 02:02:26 | 1 | ||||||
|
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 | 2026-02-14 02:02:29 | 86 | |||||||
|
cutadapt Resource Report Resource Website 5000+ mentions |
cutadapt (RRID:SCR_011841) | cutadapt | software resource | Software tool that removes adapter sequences from DNA sequencing reads., 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 required by: SL-quant works with: Trim Galore |
DOI:10.14806/ej.17.1.200 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01086, biotools:cutadapt | https://bio.tools/cutadapt | https://sources.debian.org/src/cutadapt/ | SCR_011841 | 2026-02-14 02:02:05 | 7023 | |||||
|
SynTView Resource Report Resource Website 1+ mentions |
SynTView (RRID:SCR_011939) | SynTView | software resource | An interactive multi-view genome browser for next-generation comparative microorganism genomics. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01500, biotools:syntview | https://bio.tools/syntview | SCR_011939 | 2026-02-14 02:02:16 | 7 | ||||||||
|
NeSSM Resource Report Resource Website 10+ mentions |
NeSSM (RRID:SCR_011941) | NeSSM | software resource | A Next-Generation Sequencing Simulator for Metagenomics. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01510, biotools:nessm | https://bio.tools/nessm | SCR_011941 | 2026-02-14 02:02:07 | 11 | ||||||||
|
MetaVelvet Resource Report Resource Website 50+ mentions |
MetaVelvet (RRID:SCR_011915) | MetaVelvet | software resource | Software for a short read de novo metagenome assembly created by modifying and extending a single-genome and de Bruijn-graph based assembler, Velvet. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01427, biotools:metavelvet | https://bio.tools/metavelvet | SCR_011915 | MetaVelvet: a short read assember for metagenomics | 2026-02-14 02:02:07 | 78 | |||||||
|
GeneStitch Resource Report Resource Website |
GeneStitch (RRID:SCR_011910) | GeneStitch | software resource | Network Matching Algorithm using the de Bruijn graph assembly of metagenomes to improve the assembly of genes. | gene fragment, network matching, gene assembly, metagenomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Indiana University; Indiana; USA |
PMID:22962453 | Open unspecified license | OMICS_01421, biotools:genestitch | https://bio.tools/genestitch | SCR_011910 | GeneStitch: Network Matching Algorithm to Gene Assembly | 2026-02-14 02:02:31 | 0 | |||||
|
naiveBayesCall Resource Report Resource Website |
naiveBayesCall (RRID:SCR_011866) | naiveBayesCall | software resource | An efficient model-based base-calling algorithm for high-throughput sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01152, biotools:bayescall | https://bio.tools/bayescall | SCR_011866 | 2026-02-14 02:02:06 | 0 | ||||||||
|
ABNER Resource Report Resource Website 10+ mentions |
ABNER (RRID:SCR_011868) | ABNER | software resource | A software tool for molecular biology text analysis. At ABNER''s core is a statistical machine learning system using linear-chain conditional random fields (CRFs) with a variety of orthographic and contextual features. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
biotools:abner, OMICS_01168 | https://bio.tools/abner | SCR_011868 | 2026-02-14 02:02:15 | 27 | ||||||||
|
Eoulsan Resource Report Resource Website 10+ mentions |
Eoulsan (RRID:SCR_011901) | Eoulsan | software resource | A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. | matlab, unix/linux, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22492314 | OMICS_01402, biotools:Eoulsan | https://www.outils.genomique.biologie.ens.fr/eoulsan/ https://bio.tools/Eoulsan |
SCR_011901 | 2026-02-14 02:02:16 | 22 |
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