{"id":44321,"url":"https://github.com/cmdcolin/awesome-genome-visualization","name":"awesome-genome-visualization","description":"A list of interesting genome browser and genome visualization programs","projects_count":1079,"last_synced_at":"2026-09-10T07:00:29.860Z","repository":{"id":37502562,"uuid":"228557548","full_name":"cmdcolin/awesome-genome-visualization","owner":"cmdcolin","description":"A list of interesting genome browser and genome visualization 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based","MSA","Circular","K-mer","Heatmap","Commercial","Logo","CNV","Static","Gene fusion","Alignments","Comparative","Single cell","GWAS","Dotplot","Gene structure","Microbiology","Graph","SV","based","Synthetic biology","Special-purpose","Exotic","Epigenomics","Alignments viewer","Pangenome","Splicing","Quantitative","Expression","Population","Ideogram","Protein","Historical","Methylation","Phylogenetics","Assembly QC","BLAST","Academic license","Local ancestry","Linear","Coverage","Transposons","Annotation","Repeats","Mobile app","Long reads","Hi-C","Deadlink","Chromosome painting","Uncategorized","Assembly","Manhattan","Multi-way synteny","Nanopore","Sanger","Text-based"],"sub_categories":[],"readme":"# awesome-genome-visualization\n\nA list of interesting genome visualizers, genome browsers, or\ngenome-browser-like implementations\n\nSee the new companion website here\nhttps://cmdcolin.github.io/awesome-genome-visualization/\n\nFollow the BlueSky https://bsky.app/profile/awesomegenomeviz.bsky.social or\nMastodon account https://genomic.social/@awesomegenomevisualization\n\nNote that the organization on the GitHub README here is a best effort\ncategorization using the first tag applied to each tool, but tools can have\nmultiple tags too. See the website to see all tags applied to tools\n\nThe general focus here is on tools that plot things in genomic or sequence\ncoordinate space\n\nNote: This list runs the gammut from bespoke and simple to more general-purpose\nand complex tools. Some are historical, or may be for more visual inspiration\nonly\n\nI also encourage you to make your own visualization, things like R, ggplot2,\nmatplotlib, and (the elephant in the room: coding agents, but careful with\nthese, they can hamper your learning if you become overly reliant on them) make\nthis much easier! But also consider making your visualization code re-usable for\nthe wider community! And feel free to send PRs for more tools!\n\nFinally, at least 68% (372/543) tools in this list have written publications for\ntheir tools. They went through the effort to write it up, cite these tools!!\n\n## General\n\n- [Argo](https://web.archive.org/web/20070924141423/http://www.broad.mit.edu/annotation/argo/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/argo.png)\n- [BasePlayer](https://baseplayer.fi/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/baseplayer.png)\n- [Biodalliance](http://www.biodalliance.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/biodalliance.png)\n- [Celera genome browser](https://www.csee.umbc.edu/~turner/presentations/bvw2002/sld009.htm)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/celera.jpeg)\n- [CodeXomics](https://scilence2022.github.io/CodeXomics/) (AI-native genome\n browser: conversational agents drive the view and run BLAST, primer design,\n and structure lookups; MCP server and plugin architecture included)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/codexomics.png)\n- [Ensembl genome browser](https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ensembl.png)\n- [Ensembl genome browser 2020 edition](http://2020.ensembl.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/2020ensembl.png)\n- [GBrowse 2](http://gmod.org/wiki/GBrowse) (Original gbrowse paper\n https://doi.org/10.1101/gr.403602)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gbrowse.png)\n- [GenomeMaps](http://www.genomemaps.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomemaps.jpg)\n- [Genoverse](https://github.com/wtsi-web/Genoverse)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genoverse.png)\n- [Gosling](https://gosling.js.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gosling.png)\n- [gtracks](https://gitlab.com/salk-tm/gtracks) (Powered by pyGenomeTracks)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtracks.png)\n- [HiGlass](https://higlass.io)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/higlass.png)\n- [IGB](https://bioviz.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igb.jpg)\n- [IGV](https://igv.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igv.jpg)\n- [IGV.js](https://github.com/igvteam/igv.js/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igvjs.png)\n- [JBrowse](http://jbrowse.org/jbrowse1.html) (See also JBrowse plugin registry\n https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app\n using Electron)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbrowse.png)\n- [JBrowse 2](http://jbrowse.org/jb2) (See gallery for more examples\n https://jbrowse.org/jb2/gallery)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbrowse2.png)\n- [Kero-BROWSE](https://kero.hgc.jp/examples/CLCL/hg38/index.html) (Also can\n visualize basic synteny, see tracks e.g.\n https://kero.hgc.jp/tool/keyword.html#kero:chrX:153,724,868-153,744,762 human\n vs chimp)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/kerobrowse.png)\n- [NCBI Genome Data Viewer](https://www.ncbi.nlm.nih.gov/genome/gdv/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gdv.png)\n- [Nucleome browser](https://vis.nucleome.org/v1/main.html) (github at\n https://github.com/nucleome)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nucleome.png)\n- [Pileup.js](https://github.com/hammerlab/pileup.js)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pileupjs.png)\n- [Savant](http://bioinformatics-ca.github.io/savant_genome_browser_lab_2015/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/savant.jpg)\n- [Tablet](https://ics.hutton.ac.uk/tablet/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tablet.jpeg)\n- [trackplot (python)](https://github.com/ygidtu/trackplot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackplot_python.png)\n- [Trackster](https://galaxyproject.org/learn/visualization/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackster.png)\n- [UCSC genome browser](https://genome.ucsc.edu/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ucsc.jpg)\n- [UTGB (University of Tokyo Genome Browser)](http://utgenome.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/utgb.png)\n- [Valis browser](https://valis.bio/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/valis.png)\n- [WashU epigenomics browser](https://epigenomegateway.wustl.edu/) (The ReactJS\n is a redesign, there is also a legacy version. Note also, there are\n comparative features\n https://www.biorxiv.org/content/10.1101/2022.11.29.518374v1)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/washu.png)\n- [Zenbu](http://fantom.gsc.riken.jp/zenbu/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/zenbu.png)\n\n## Alignments\n\n- [alignoth](http://htmlpreview.github.io/?https://github.com/koesterlab/alignoth/blob/main/examples/plot.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignoth.png)\n- [bamscope](https://github.com/jslfree080/bamscope)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamscope.png)\n- [Chromatic](https://chromatic.nci.nih.gov/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromatic.png)\n- [DrukBam](https://github.com/StephanHolgerD/DrukBam)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/drukbam.png)\n- [Gambit](http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gambit.png)\n- [GenomeView (java app)](https://genomeview.org/content/quick-start-guide)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeview_java.png)\n- [gw](https://github.com/kcleal/gw)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gw.png)\n- [Hawkeye](https://github.com/peterhj/amos)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hawkeye.png)\n- [LookSeq](https://www.sanger.ac.uk/tool/lookseq/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lookseq.png)\n- [MagicViewer](http://bioinformatics.zj.cn/magicviewer/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/magicviewer.jpeg)\n- [MapView](https://web.archive.org/web/20201023093840/https://sites.google.com/site/wjwdavymapview/mapview/MapView.zip?attredirects=0)\n (URL is a direct link to zip file download on archive.org)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mapview.jpg)\n- [NGB](https://github.com/epam/NGB)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ngb.png)\n- [pyBamView](https://mgymrek.github.io/pybamview/) (See supplementary info for\n more figures, supports padded SAM/BAM which is fairly rare)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pybamview.png)\n- [Staden](https://sourceforge.net/projects/staden/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/staden.png)\n- [udon](https://github.com/ocxtal/udon) (Uses an advanced data structure for\n pileup, so visually a basic example but likely just a small demo)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/udon.png)\n- [wally](https://github.com/tobiasrausch/wally) (Available via the web from\n compiling to wasm)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wally.png)\n\n## Annotation\n\n- [Varsome](\u003chttps://varsome.com/security-validation/?next=/variant/hg19/NM_000088.3(COL1A1):c.658C%3ET\u003e)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/varsome.png)\n\n## Assembly QC\n\n- [ALVIS (chimeric alignment viewer)](https://github.com/SR-Martin/alvis)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alvis_chimeric.png)\n- [Consed](http://bozeman.mbt.washington.edu/consed/consed.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/consed.png)\n- [GCI](https://github.com/yeeus/GCI)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gci.jpg)\n- [Genome Puzzle Master (GPM)](https://jianwei-zhang.github.io/LIMS/GPM-Manual.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gpm.png)\n- [Icarus QUAST](http://quast.sourceforge.net/icarus.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/icarus.png)\n- [MIRA](http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html)\n (orig paper also describes mira here\n http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465\u0026rep=rep1\u0026type=pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mira.png)\n- [vega](http://vega.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=6-QBL)\n (Mentioned in\n https://www.biorxiv.org/content/10.1101/2021.07.02.450883v1.full.pdf also\n note: vega standards for vertebrate genome annotation database)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vega.png)\n\n## BLAST\n\n- [SequenceServer](https://sequenceserver.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequenceserver.png)\n\n## Chromosome painting\n\n- [GeMo](https://github.com/SouthGreenPlatform/GeMo)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gemo.png)\n\n## Circular\n\n- [Anvio](https://peerj.com/articles/1319/)\n- [BioCircos.js](http://bioinfo.ibp.ac.cn/biocircos/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/biocircos.png)\n- [BRICK (BRIG-like circular knowledgebase)](https://brick.ink/) (See also BRIG)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/brick.png)\n- [CGView](http://cgview.ca/) (See also CGView comparison tool and other related\n https://paulstothard.github.io/cgview_comparison_tool/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgview.png)\n- [CGView.js](https://js.cgview.ca/) (Used by proksee)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgviewjs.png)\n- [Circleator](http://jonathancrabtree.github.io/Circleator/index.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circleator.png)\n- [circlize](https://github.com/jokergoo/circlize)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circlize.jpeg)\n- [Circos](http://circos.ca/) (no official github to my knowledge)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circos.png)\n- [CircosJS](https://github.com/nicgirault/circosJS)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circosjs.png)\n- [circularMT](https://github.com/msjimc/circularMT)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circularmt.png)\n- [DNAPlotter](https://www.sanger.ac.uk/science/tools/dnaplotter)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaplotter.jpg)\n- [GenomeProjector](https://github.com/gaou/g-language/wiki)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/glanguage.jpg)\n- [genoVi](https://github.com/robotoD/GenoVi)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genovi.png)\n- [Gview](https://server.gview.ca/examples)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gview.png)\n- [JupiterPlot](https://github.com/JustinChu/JupiterPlot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jupiterplot.png)\n- [OGDRAW](https://chlorobox.mpimp-golm.mpg.de/OGDraw.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ogdraw.png)\n- [OmicCircos](http://bioconductor.org/packages/release/bioc/html/OmicCircos.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/omiccircos.png)\n- [pyCirclize](https://github.com/moshi4/pyCirclize)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pycirclize.png)\n- [pyCircos](https://github.com/ponnhide/pyCircos) (See also\n https://github.com/ponnhide/plasmidviewer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pycircos.png)\n- [RegulomeExplorer](http://explorer.cancerregulome.org/all_pairs/?dataset=TCGA_ACC)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cancerregulome.png)\n\n## CNV\n\n- [aCNVViewer](https://github.com/FJD-CEPH/aCNViewer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/acnvviewer.png)\n- [BAMScale](https://github.com/ncbi/BAMscale)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamscale.png)\n- [bcftools cnv](https://samtools.github.io/bcftools/howtos/cnv-calling.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bcftools_cnv.png)\n- [CNANorm](https://www.bioconductor.org/packages/release/bioc/html/CNAnorm.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnanorm.png)\n- [CNSpector](https://github.com/PapenfussLab/CNspector)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnspector.png)\n- [cnvCurator](http://www.acsu.buffalo.edu/~lm69/cnvCurator)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvcurator.png)\n- [CNVkit](https://cnvkit.readthedocs.io/en/stable/plots.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvkit.png)\n- [copynumber](https://www.bioconductor.org/packages/release/bioc/vignettes/copynumber/inst/doc/copynumber.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/copynumber.png)\n- [CoveragePlotter](http://lindenb.github.io/jvarkit/CoveragePlotter.html) (See\n also http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html for\n multi-chromosome)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/coverageplotter.png)\n- [covviz](https://brwnj.github.io/covviz/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/covviz.png)\n- [genevisR](https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genevisr.png)\n- [genome_coverage_plotter](https://github.com/matted/genome_coverage_plotter)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome-coverage-plotter.png)\n- [GenomePaint](https://genomepaint.stjude.cloud/) (Demos\n https://proteinpaint.stjude.org/bam/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomepaint.png)\n- [GenomeSpy](https://genomespy.app/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomespy.png)\n- [Genovar](http://genovar.sourceforge.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genovar.png)\n- [mocha](https://github.com/freeseek/mocha) (Has a full analysis pipeline\n associated with end result visualizations)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mocha.png)\n- [Orchestral](undefined)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/orchestral.png)\n- [PURPLE](https://github.com/hartwigmedical/hmftools/blob/master/purity-ploidy-estimator/README.md)\n (intermutation-distance rainfall plots/katagesis plots are not technically in\n genomic coordinates, but do indicate genomic cluster of variants)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/purple.png)\n- [SeeNV](https://github.com/MSBradshaw/SeeNV)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seenv.png)\n- [sequenza](https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html#plots-and-results)\n (also see https://sequenzatools.bitbucket.io/#/home)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequenza.png)\n- [SFARI](https://gene.sfari.org/database/human-gene/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sfari.jpg)\n- [SnoopCGH](http://snoopcgh.sourceforge.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snoopcgh.jpg)\n- [SNPitty](https://bitbucket.org/ccbc/snpitty/src/master/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpitty.jpg)\n\n## Commercial\n\n- [10x genomics - Loupe](https://support.10xgenomics.com/genome-exome/software/visualization/latest/structural-variants)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/10xgenomics.png)\n- [Alamut](https://www.interactive-biosoftware.com/alamut-visual/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alamut.png)\n- [ATCC Genome Portal](https://docs.onecodex.com/en/articles/3996697-using-the-genome-browser)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/atcc.png)\n- [Benchling](https://www.benchling.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/benchling.png)\n- [Bionano](https://bionanogenomics.com/technology/structural-variation/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bionano.png)\n- [Circa](https://omgenomics.com/circa)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/circa.png)\n- [CLC Genomics workbench](https://digitalinsights.qiagen.com/news/blog/discovery/structural-variant-detection-using-clc-genomics-workbench/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/clcgenomics.png)\n- [DNASTAR](https://www.dnastar.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnastar.png)\n- [ERGO](https://www.igenbio.com/ergo)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ergo.png)\n- [Geneious](https://www.geneious.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneious.png)\n- [Genestack](https://genestack.com/blog/2015/05/28/navigation-in-genestack-genome-browser/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genestack.png)\n- [Golden Helix](https://www.goldenhelix.com/products/GenomeBrowse/) (Free for\n academic use)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/goldenhelix.png)\n- [Lucid viewer](https://lucidalign.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lucidalign.png)\n- [MacVector](https://macvector.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/macvector.png)\n- [Persephone](https://persephonesoft.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/persephone.jpg)\n- [SnapGene](https://www.snapgene.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snapgene.png)\n- [Strand NGS](https://www.strand-ngs.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/strandngs.png)\n\n## Comparative\n\n- [AccuSyn](https://accusyn.usask.ca/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/accusyn.png)\n- [Aequatus](https://github.com/TGAC/Aequatus)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aequatus.png)\n- [AliTV](https://alitvteam.github.io/AliTV/d3/AliTV.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alitv.png)\n- [Artemis comparison tool (ACT)](https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/artemis_act.png)\n- [asynt](https://github.com/simonhmartin/asynt)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/asynt.png)\n- [AutoGraph](http://autograph.genouest.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/autograph.png)\n- [BactoGENIE](undefined)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bactogenie.png)\n- [Biodalliance comparative demo](http://biodalliance.org/dev/test-comparative.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/biodalliance_comparative.png)\n- [BRIG](http://brig.sourceforge.net)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/brig.jpg)\n- [Chromatiblock](https://github.com/mjsull/chromatiblock)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromatiblock.png)\n- [CHROMEISTER](https://github.com/estebanpw/chromeister)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromeister.png)\n- [chromoMap](https://lakshay-anand.github.io/chromoMap/index.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromomap.png)\n- [chromsyn](https://github.com/slimsuite/chromsyn)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromsyn.png)\n- [Cinteny](http://cinteny.cchmc.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cinteny.png)\n- [clinker](https://github.com/gamcil/clinker)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/clinker.png)\n- [CMap](http://gmod.org/wiki/CMap)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cmap.jpg)\n- [CoGe](https://genomevolution.org/coge/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/coge.png)\n- [Combo](undefined) (Based on the tool 'Argo')\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/combo.png)\n- [Comparative assembly hub snake track](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/comparative_assembly_hub.png)\n- [CrossBrowse](https://github.com/shenkers/CrossBrowse)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/crossbrowse.png)\n- [CrowsNest](https://pgsb.helmholtz-muenchen.de/crowsnest/help.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/crowsnest.png)\n- [CVit](https://sourceforge.net/projects/cvit/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cvit.png)\n- [Cvit.js](https://github.com/LegumeFederation/cvitjs)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cvitjs.png)\n- [EasyFig](https://mjsull.github.io/Easyfig/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/easyfig.png)\n- [EvolutionHighway](http://eh-demo.ncsa.illinois.edu/) (The 'evolutionary\n highway' image type is reproduced in some other packages e.g.\n https://github.com/marta-fb/syntenyPlotteR, paper\n https://doi.org/10.1126/science.1111387)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/evolutionaryhighway.jpg)\n- [FastANI](https://github.com/ParBLiSS/FastANI)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/fastani.jpg)\n- [gbdraw](https://github.com/satoshikawato/gbdraw)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gbdraw.png)\n- [GBrowse_syn](http://gmod.org/wiki/GBrowse_syn)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gbrowse_syn.png)\n- [GCSnap](https://github.com/JoanaMPereira/GCsnap)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gcsnap.png)\n- [GENESPACE](https://github.com/jtlovell/GENESPACE/) (Note: plots in 'gene\n space' instead of actual genome coordinates. Includes a powerful analysis\n pipeline, worth reading the paper. See also DEEPSPACE, which uses genome\n coordinates and whole genome alignments)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genespace.png)\n- [Genome Context Viewer](https://www.legumefederation.org/gcv/phytozome_10_2/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome_context_viewer.png)\n- [Genome-plots-processing](https://github.com/filip-husnik/genome-plots-processing)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genome_plots_processing.png)\n- [GenomeMatcher](http://www.ige.tohoku.ac.jp/joho/gmProject/gmmanual.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomematcher.png)\n- [GenomeSyn](https://github.com/jmsong2/GenomeSyn)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomesyn.png)\n- [GenomicBreaks](https://oist.github.io/GenomicBreaks/articles/GenomicBreaks.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomicbreaks.png)\n- [Genomicus](https://www.genomicus.biologie.ens.fr/genomicus/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomicus.png)\n- [gggenomes](https://github.com/thackl/gggenomes)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gggenomes.png)\n- [GGisy](https://github.com/Sanrrone/GGisy)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggisy.png)\n- [GIVE](https://zhong-lab-ucsd.github.io/GIVE_homepage/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/give_hic.png)\n- [Gmaj](https://www.bx.psu.edu/miller_lab/dist/CHAP/docs/gmaj_geneconv.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gmaj.png)\n- [GSSPlayground](https://github.com/orangeSi/GSSplayground)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gssplayground.png)\n- [JAX Synteny browser](https://github.com/TheJacksonLaboratory/syntenybrowser)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jax_synteny_browser.png)\n- [LinearDisplay.pl](https://github.com/JCVenterInstitute/LinearDisplay) (readme\n says to cite this paper)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lineardisplay.png)\n- [mauve-viewer](https://github.com/nconrad/mauve-viewer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mauve_viewer.png)\n- [MCScan (python version)](\u003chttps://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)\u003e)\n (Also has 2024 citation here\n https://onlinelibrary.wiley.com/doi/10.1002/imt2.211)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcscan_python.png)\n- [MCScanX](https://github.com/wyp1125/MCScanX)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcscanx.png)\n- [mGSV (multiple genome synteny viewer)](https://github.com/kashmatic/mGSV)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mgsv.jpg)\n- [miropeats](http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/)\n (image from 2021 paper\n https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/miropeats.png)\n- [MizBee](http://www.cs.utah.edu/~miriah/mizbee/Overview.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mizbee.jpg)\n- [ModDotPlot](https://github.com/marbl/ModDotPlot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/moddotplot.png)\n- [multiGenomicContext](https://github.com/Sanrrone/multiGenomicContext)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/multicontext.png)\n- [Multiple genome viewer](http://www.informatics.jax.org/mgv/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mgv.png)\n- [NCBI CGV](https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/05/cgv-beta-release/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgv.png)\n- [NGenomeSyn](https://github.com/hewm2008/NGenomeSyn) (See also RectChr)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ngenomesyn.png)\n- [ntSynt](https://github.com/bcgsc/ntSynt-viz) (Uses gggenomes)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ntsynt.png)\n- [odp (oxford dot plots)](https://github.com/conchoecia/odp) (Pub is not for\n visualization tool, but it is suggested to cite this paper)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/odp.png)\n- [OMA local synteny browser](https://omabrowser.org/oma/synteny/ADH1A_HUMAN/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/oma.png)\n- [paf2dot](https://github.com/pangenome/paf2dot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/paf2dot.png)\n- [paf2dotplot](https://github.com/moold/paf2dotplot) (Based on dotPlotly)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/paf2dotplot.png)\n- [pafr](https://github.com/dwinter/pafr)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pafr.png)\n- [Parasight](https://baileylab.brown.edu/parasight/galframe.html) (Examples at\n https://ratparalogy.gs.washington.edu/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/parasight.png)\n- [PipMaker](http://pipmaker.bx.psu.edu/pipmaker/) (See also MultiPipMaker\n http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pipmaker.png)\n- [plotsr](https://github.com/schneebergerlab/plotsr) (see also\n https://github.com/schneebergerlab/syri)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotsr.png)\n- [pretzel](https://github.com/plantinformatics/pretzel)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pretzel.png)\n- [progressiveMauve viewer](http://darlinglab.org/mauve/user-guide/viewer.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/progressive_mauve.png)\n- [PSAT](http://www.nwrce.org/psat)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/psat.png)\n- [pyGenomeViz](https://github.com/moshi4/pyGenomeViz) (See also\n https://github.com/moshi4/MGCplotter https://github.com/moshi4/GBKviz\n https://github.com/moshi4/plot_genome_align_fig)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygenomeviz.png)\n- [QUAAK](https://github.com/YingZhou001/Quaak) (Quick Unique k-mer Assembly\n Assessment Kit. Uses unique k-mers to compare reference and query genomes,\n building synteny blocks to assess assembly completeness and flag large\n structural variations. Outputs reference-centric block-mapping plots. Sample\n image from\n https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=submissions/76E3F239-A9A6-4B6B-840F-B49053807394--R3_verkko-v2.3.2_hybrid_assembly_qc/HG00146/quaak/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/quaak.png)\n- [r2cat](https://github.com/phuseman/r2cat)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/r2cat.jpeg)\n- [RectChr](https://github.com/BGI-shenzhen/RectChr)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rectchr.png)\n- [SafFire](https://mrvollger.github.io/SafFire/#ref=CHM13_v1.1\u0026query=GRCh38)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/saffire.png)\n- [SequenceSurveyor](https://graphics.cs.wisc.edu/Vis/SequenceSurveyor/index.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequencesurveyor.png)\n- [ShinySyn](undefined)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/shinysyn.png)\n- [SimpleSynteny](https://www.dveltri.com/simplesynteny/about.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/simplesynteny.jpg)\n- [Smash++](https://github.com/smortezah/smashpp)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/smashpp.png)\n- [Sybil](http://sybil.sourceforge.net/) (Download\n https://sourceforge.net/projects/sybil/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sybil.png)\n- [SyMap](http://www.agcol.arizona.edu/software/symap/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/symap.png)\n- [SynBrowse](undefined)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/synbrowse.png)\n- [Synima](https://github.com/rhysf/Synima)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/synima.png)\n- [syntenyPlotteR](https://github.com/marta-fb/syntenyPlotteR)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntenyplotter.png)\n- [SyntenyPortal](http://bioinfo.konkuk.ac.kr/synteny_portal/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntenyportal.png)\n- [syntR](https://www.samuklab.com/syntR/articles/syntr_tutorial.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntr.png)\n- [SynTView](http://hub18.hosting.pasteur.fr/SynTView/documentation/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syntview.png)\n- [SynVisio](https://synvisio.github.io/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/synvisio.png)\n- [SYNY](https://github.com/PombertLab/SYNY)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/syny.png)\n- [TidyLocalSynteny](https://github.com/cxli233/TidyLocalSynteny)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tidylocalsynteny.png)\n- [TreeBrowser (MicrobesOnline)](http://www.microbesonline.org/cgi-bin/treeBrowse.cgi?locus=17761)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/treegenome.png)\n- [Tripal MapViewer](https://github.com/statonlab/tripal_map)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tripal_mapviewer.png)\n- [VISTA browser](http://pipeline.lbl.gov/cgi-bin/gateway2)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vista.png)\n- [WGDI](https://github.com/SunPengChuan/wgdi)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wgdi.png)\n- [XMatchView](https://www.bcgsc.ca/resources/software/xmatchview)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/xmatchview.png)\n- [ziplign](https://github.com/martinghunt/ziplign) (ACT (Artemis Comparison\n Tool) replacement)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tna.png)\n\n## Coverage\n\n- [BAMdash](https://github.com/jonas-fuchs/BAMdash/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamdash.png)\n- [dep](https://github.com/slw287r/dep) (Can handle very deep coverage)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dep.png)\n- [ggcoverage](https://cran.r-project.org/web/packages/ggcoverage/vignettes/ggcoverage.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggcoverage.png)\n- [SeqCover](https://brentp.github.io/seqcover/#gene=AIFM1)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqcover.png)\n- [signac](https://github.com/timoast/signac/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/signac.png)\n- [Trackplot (R)](https://github.com/PoisonAlien/trackplot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackplot.png)\n- [wiggleplotr](http://bioconductor.org/packages/devel/bioc/vignettes/wiggleplotr/inst/doc/wiggleplotr.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wiggleplotr.png)\n\n## Deadlink\n\n- [CGH-Explorer](undefined)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cghexplorer.jpg)\n- [DNAVis](undefined)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnavis.png)\n- [VAMP](undefined)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vamp.jpg)\n\n## Dotplot\n\n- [D-GENIES](http://dgenies.toulouse.inra.fr/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dgenies.png)\n- [DAGchainer](http://dagchainer.sourceforge.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dagchainer.png)\n- [Delly-maze](https://github.com/dellytools/maze) (see also\n https://www.gear-genomics.com/maze/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/maze.png)\n- [Discoplot](https://github.com/mjsull/DiscoPlot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/discoplot.png)\n- [Dot](https://dot.sandbox.bio/) (Python data preparation script)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dot.png)\n- [Dotlet](https://dotlet.vital-it.ch/) (The original publication was 2000 but\n updated ~2020 with reactjs)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotlet.png)\n- [Dotplot (chirimoyo)](https://chirimoyo.ac.uma.es/bitlab/portfolio/dotplot/)\n- [dotPlotly](https://github.com/tpoorten/dotPlotly/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotplotly.png)\n- [Dotter](https://sonnhammer.sbc.su.se/Dotter.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dotter.png)\n- [Dottup](https://www.bioinformatics.nl/cgi-bin/emboss/help/dottup) (also seen\n here\n http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dottup.png)\n- [FlexiDot](https://github.com/molbio-dresden/flexidot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/flexidot.png)\n- [Gepard](http://cube.univie.ac.at/gepard)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gepard.jpeg)\n- [ggplot2 mummerplot](https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummerplot_ggplot2.png)\n- [iLambda Dotplot](https://github.com/iLambda/dotplot)\n- [Jdot](https://github.com/LyonsLab/jdot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jdot.png)\n- [JGI IMG](https://img.jgi.doe.gov/) (Dotplot use MUMmer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jgiimg.png)\n- [last-dotplot](https://gitlab.com/mcfrith/last)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/last_dotplot.png)\n- [local-rearrangements](https://github.com/mcfrith/local-rearrangements) (Can\n color dotplots with annotations for e.g. exons, transposons, low complexity\n regions. See also last-dotplot. Nice figure using it here\n https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00762-1/figures/4)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/local-rearrangements.png)\n- [MashMap](https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mashmap.png)\n- [mcutils](https://github.com/mchaisso/mcutils)\n (https://twitter.com/mjpchaisson/status/1040363992206569472)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcutils_dotplot.jpeg)\n- [Minidot](https://github.com/thackl/minidot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/minidot.png)\n- [Mummer-idotplot](https://github.com/ryought/mummer-idotplot)\n- [Mummerplot](http://mummer.sourceforge.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummerplot.png)\n- [oxford-plots](https://github.com/jherrero/oxford-plots) (Has nice description\n of a synteny pipeline here\n https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/oxford.png)\n- [Redotable](https://github.com/s-andrews/redotable)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/redotable.png)\n- [shinyChromosome](http://150.109.59.144:3838/shinyChromosome/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/shinychromosome.png)\n- [syntenyPlotByR](https://github.com/shingocat/syntenyPlotByR)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/synteny_plot_by_r.png)\n\n## Epigenomics\n\n- [Chip Monk](http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/) (Also\n see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chipmonk.png)\n- [Chipster](https://chipster.csc.fi/) (Copy number tutorial\n https://chipster.csc.fi/manual/cn-tutorial.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chipster.jpg)\n- [cisGenome Browser](https://jhui2014.github.io/browser/screenshots.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cisgenome.png)\n- [CoolBox](https://github.com/GangCaoLab/CoolBox) (fork of pyGenomeTracks)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/coolbox.png)\n- [EaSeq](https://easeq.net/screenshots/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/easeq.png)\n- [Epilogos](https://epilogos.altius.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/epilogos.jpg)\n- [Epiviz](https://epiviz.github.io/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/epiviz.png)\n- [HiPiler](http://hipiler.higlass.io)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hipiler.png)\n- [JBR](https://artyomovlab.wustl.edu/jbr/2018_h3k27ac_aging/) (Not open source,\n at least not on github)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jbr.png)\n- [Juicebox](https://github.com/aidenlab/Juicebox)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/juicebox.jpg)\n- [Juicebox.js](http://www.igv.org/doc/juiceboxjs.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/juiceboxjs.jpg)\n- [Peax](https://github.com/Novartis/peax)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/peax.png)\n- [python-genome-browser aka pygbrowse](https://github.com/phageghost/python-genome-browser/blob/master/pygbrowse_demonstration.ipynb)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygbrowse.png)\n\n## Exotic\n\n- [BigTop](https://blog.dnanexus.com/2019-05-21-bigtop-data-visualization/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bigtop.png)\n- [Cylindrical alignment app](https://sourceforge.net/projects/cylindrical-alignment-app/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cylindrical_alignment_viewer.png)\n- [DNASkittle](https://www.dnaskittle.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaskittle.png)\n- [FluentDNA](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203487/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/fluentdna.jpeg)\n- [sockeye](https://www.bcgsc.ca/resources/software/sockeye)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sockeye.jpg)\n- [spinteny](https://github.com/skinner/spinteny)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/spinteny.png)\n\n## Expression\n\n- [GTEX Locus browser](https://gtexportal.org/home/locusBrowserPage/ACTN3)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtex_locus.png)\n\n## Gene fusion\n\n- [AGFusion](https://github.com/murphycj/AGFusion) (See also\n https://www.agfusion.app/ for web based version)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/agfusion.png)\n- [arriba](https://github.com/suhrig/arriba)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/arriba.png)\n- [Chimeraviz](https://github.com/stianlagstad/chimeraviz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chimeraviz.png)\n- [clinker (gene fusion software)](https://github.com/Oshlack/Clinker/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/clinker_fusion.png)\n- [FusionInspector](https://github.com/FusionInspector/FusionInspector/wiki)\n (Uses igv.js)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/fusioninspector.png)\n- [GeneFuse](https://opengene.org/GeneFuse/report.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genefuse.png)\n- [MAVIS](http://mavis.bcgsc.ca/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mavis.png)\n\n## Gene structure\n\n- [Apollo aka WebApollo](https://genomearchitect.readthedocs.io/en/latest/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/webapollo.jpg)\n- [D3GB](http://d3gb.usal.es/) (Live link\n http://d3gb.usal.es/docs/HumanGenomeBrowser/index.html?r=12:121113963-121213963\n doesn't work anymore)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/d3gb.png)\n- [ggtranscript](https://github.com/dzhang32/ggtranscript)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggtranscript.png)\n- [TnT](https://tnt.marlin.pub/articles/introduction)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tnt.png)\n\n## Graph\n\n- [AGB assembly graph browser](https://github.com/almiheenko/AGB)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/agb.jpeg)\n- [Bandage](https://github.com/rrwick/Bandage/) (See also BandageNG\n https://github.com/asl/BandageNG)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bandage.png)\n- [ctag](https://github.com/AbeelLab/ctag) (See also hygene\n https://github.com/ProgrammingLife2017/hygene)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ctag.png)\n- [gfaestus](https://github.com/chfi/gfaestus) (See demo video displaying GFF3\n annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gfaestus.png)\n- [gfalook](https://github.com/pangenome/gfalook) (See also odgi viz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gfalook.png)\n- [GfaViz](https://github.com/ggonnella/gfaviz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gfaviz.png)\n- [graphgenomeviewer](https://cmdcolin.github.io/graphgenomeviewer/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/graphgenomeviewer.png)\n- [IGGE](https://github.com/immersivegraphgenomeexplorer/IGGE) (Not open source)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igge.png)\n- [LINX](https://github.com/hartwigmedical/hmftools/tree/master/linx) (part of\n the PURPLE/GRIDSS/LINX pipeline)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/linx.png)\n- [MoMi-G](https://github.com/MoMI-G/MoMI-G)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/momig.png)\n- [odgi draw + odgi viz + odgi inject](https://odgi.readthedocs.io/en/latest/index.html)\n (Example from https://github.com/pangenome/pggb, see also gene arrow map\n https://odgi.readthedocs.io/en/latest/rst/tutorials/injecting_gene_arrows.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/odgi.png)\n- [panGraphViewer](https://github.com/TF-Chan-Lab/panGraphViewer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pangraphviewer.jpg)\n- [PangyPlot](https://github.com/ScottMastro/pangyplot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pangyplot.png)\n- [PGR-TK](https://github.com/cschin/pgr-tk)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgrtk.png)\n- [pgv (graph tool)](https://w-gao.github.io/pgv/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgv2.png)\n- [sequence tube map](https://github.com/vgteam/sequenceTubeMap)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sequence_tube_map.png)\n- [SGTK (scaffold graph toolkit)](https://olga24912.github.io/SGTK/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sgtk.png)\n- [Shasta](https://chanzuckerberg.github.io/shasta/ComputationalMethods.html#ReadGraph)\n (Uses graphviz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/shasta.png)\n- [strangepg](https://github.com/qwx9/strangepg)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/strangepg.png)\n- [VAG](https://github.com/lipingfangs/VAG)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vag.jpg)\n- [VRPG](https://github.com/codeatcg/VRPG)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vrpg.png)\n- [waragraph](https://chfi.github.io/waragraph/) (Deployed to the web via wasm)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/waragraph.png)\n\n## GWAS\n\n- [CMPlot](https://github.com/YinLiLin/CMplot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cmplot.png)\n- [GeneticsMakie.jl](https://github.com/mmkim1210/GeneticsMakie.jl)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneticsmakie.png)\n- [ggplot2 manhattan plot](https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/)\n (This is not a preconfigured tool but a blog post tutorial with tidy data and\n ggplot2)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggplot2_manhattan.png)\n- [LDBlockShow](https://github.com/BGI-shenzhen/LDBlockShow)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ldblockshow.png)\n- [Locuszoom](http://locuszoom.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/locuszoom.png)\n- [Locuszoom.js](http://locuszoom.org/locuszoomjs.php)\n- [PureScript genetics browser](https://github.com/chfi/purescript-genetics-browser)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/purescript.png)\n\n## Heatmap\n\n- [UCSC Xena](https://xena.ucsc.edu/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/xena.png)\n- [VIVA](https://www.biorxiv.org/content/10.1101/589879v1.full.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/viva.png)\n\n## Hi-C\n\n- [aplot](https://yulab-smu.top/aplot/cases.html#genomics-track-example)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aplot.png)\n- [figeno](https://github.com/CompEpigen/figeno)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/figeno.png)\n- [gcMapExplorer](https://github.com/rjdkmr/gcMapExplorer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gcmapexplorer.png)\n- [Plotgardener](https://github.com/PhanstielLab/plotgardener/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotgardener.png)\n- [PretextView](https://github.com/wtsi-hpag/PretextView)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pretextview.jpg)\n\n## Historical\n\n- [ABrowse (genome browser)](undefined) (Had integrations with BioMart, Taverna)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/abrowse2.png)\n- [Apollo](https://web.archive.org/web/20060927154956/http://www.fruitfly.org/annot/apollo/)\n (URL is an archive.org link)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/apollo.jpg)\n- [gff2ps](https://genome.crg.es/software/gfftools/GFF2PS.html) (Used to make\n original figures for the human Celera genome)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gff2ps.png)\n- [Internet Contig Explorer](https://www.bcgsc.ca/resources/software/ice)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/internet_contig_explorer.jpg)\n\n## Ideogram\n\n- [chromPlot](https://www.bioconductor.org/packages/release/bioc/vignettes/chromPlot/inst/doc/chromPlot.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chromplot.png)\n- [chrov](https://github.com/rraadd88/chrov) (See also usage in\n https://github.com/rraadd88/beditor)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chrov.png)\n- [eweitz Ideogram](https://github.com/eweitz/ideogram)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/eweitz_ideogram.png)\n- [ezcharts](https://github.com/epi2me-labs/ezcharts)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ezcharts.png)\n- [Flash Gviewer](http://gmod.org/wiki/Flashgviewer/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/flashgviewer.png)\n- [genomegraphs](http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomegraphs.png)\n- [Ideogram](https://github.com/RCollins13/HumanIdiogramLibrary)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rcollins_ideogram.png)\n- [Ideogram viewer](https://bioinformatics.mdanderson.org/public-software/ideogramviewer/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ideogramviewer.png)\n- [Ideoplot](https://github.com/mchaisso/Ideoplot)\n- [IdeoViz](https://www.bioconductor.org/packages/release/bioc/vignettes/IdeoViz/inst/doc/Vignette.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ideoviz.png)\n- [karyoploteR](https://github.com/bernatgel/karyoploteR)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/karyoploter.png)\n- [KaryotypeSVG](https://github.com/andreasprlic/karyotypeSVG)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/karyotypesvg.png)\n- [NCBI Genome Decoration](undefined) (Was located at\n https://www.ncbi.nlm.nih.gov/genome/tools/gdp/, sunsetted in 2023)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ncbi_genome_decoration.png)\n- [PhenoGram](https://ritchielab.org/software/phenogram-downloads) (Can be web\n server or download)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/phenogram.png)\n- [pyideogram](https://github.com/Balthasar-eu/pyideogram)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pyideogram.png)\n- [RIdeogram](https://github.com/TickingClock1992/RIdeogram)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rideogram.png)\n- [tagore](https://github.com/jordanlab/tagore)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tagore.png)\n- [UCSC Genome Graphs](http://genome.ucsc.edu/cgi-bin/hgGenome)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ucsc_genome_graph.png)\n\n## K-mer\n\n- [Panagram](https://github.com/kjenike/panagram)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panagram.png)\n\n## Linear\n\n- [Gnomad browser](https://github.com/macarthur-lab/gnomadjs)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gnomad.png)\n\n## Local ancestry\n\n- [fineSTRUCTURE aka ChromoPainter](http://www.paintmychromosomes.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/finestructure.png)\n- [MOSAIC](https://maths.ucd.ie/~mst/MOSAIC/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mosaic.png)\n- [winpca](https://github.com/MoritzBlumer/winpca)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/winpca.png)\n\n## Logo\n\n- [LogoJS](https://logojs.wenglab.org/app/gallery/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/logojs.png)\n\n## Long reads\n\n- [methylartist](https://github.com/adamewing/methylartist)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/methylartist.png)\n\n## Manhattan\n\n- [ggwas](https://bczech.github.io/ggwas/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggwas.png)\n- [locuszoomr](https://cran.r-project.org/web/packages/locuszoomr/vignettes/locuszoomr.html)\n (See also easylabel for manhattan plots\n https://cran.r-project.org/web/packages/easylabel/vignettes/easylabel.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/locuszoomr.jpg)\n- [topr](https://github.com/totajuliusd/topr/) (Includes locuszoom style plot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/topr.png)\n\n## Methylation\n\n- [AnnoJ](https://brainome.ucsd.edu/howto_annoj.html) (See list of instances of\n the browser here https://ecker.salk.edu/genome-browser/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/annoj.png)\n- [modbamtools](https://github.com/rrazaghi/modbamtools)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/modbamtools.png)\n- [NanoMethViz](http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nanomethviz.png)\n\n## Microbiology\n\n- [clonifier](https://dlesl.github.io/clonifier/) (per github: 'A web app for\n viewing plasmid maps \u0026 genomes, and simulating PCR and Gibson assembly')\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/clonifier.png)\n- [DnaFeaturesViewer](https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer)\n (See also https://github.com/Edinburgh-Genome-Foundry/Caravagene)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnafeaturesviewer.png)\n- [GECO](http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geco.png)\n- [GeCoViz](https://gecoviz.cgmlab.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gecoviz.png)\n- [GeneViTo](http://athina.biol.uoa.gr/bioinformatics/GENEVITO/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genevito.jpg)\n- [IslandViewer and IslandPlot](https://bl.ocks.org/lairdm/c6c235dbfa6e6ee61565)\n (web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/islandplot.png)\n- [lovis4u](https://github.com/art-egorov/lovis4u)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lovis4u.png)\n\n## Mobile app\n\n- [iGenomics](https://github.com/stuckinaboot/iGenomics)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/igenomics.png)\n\n## MSA\n\n- [AA (alignment annotator)](http://www.bioinformatics.org/strap/aa) (also see\n STRAP) [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aa.png)\n- [abrowse (MSA viewer)](https://github.com/ihh/abrowse)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/abrowse.png)\n- [alen](https://github.com/jakobnissen/alen)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alen.png)\n- [alignfigR](https://cran.r-project.org/web/packages/alignfigR/vignettes/my-vignette.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignfigr.png)\n- [alignment.js](https://github.com/veg/alignment.js)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentjs.png)\n- [AlignmentComparator](http://bioinfweb.info/AlignmentComparator/) (Uses\n http://bioinfweb.info/LibrAlign/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentcomparator.png)\n- [AlignmentViewer](https://alignmentviewer.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alignmentviewer.png)\n- [AliTreeViz](https://www.npmjs.com/package/alitreeviz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alitreeviz.png)\n- [AliView](http://www.ormbunkar.se/aliview/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aliview.png)\n- [ALVIS (MSA viewer)](https://www.ebi.ac.uk/research/goldman/software/alvis)\n (Introduces sequence bundles concept, also see web app version\n https://www.ebi.ac.uk/goldman-srv/sequencebundles/ source code\n https://bitbucket.org/schwarzlab/alvis/src/master/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alvis.png)\n- [BioJS MSA](https://msa.biojs.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/biojsmsa.png)\n- [Boxshade](https://embnet.vital-it.ch/software/BOX_form.html) (Also available\n as a command line tool with `apt install boxshade`. See also rMSA which can\n automate running boxshade from within R)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/boxshade.png)\n- [CIAlign](https://github.com/KatyBrown/CIAlign) (Has useful utility functions\n to clean gaps and trim MSAs)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cialign.png)\n- [CView](https://sourceforge.net/projects/cview/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cview.png)\n- [ESPript](http://espript.ibcp.fr/ESPript/ESPript/) (Primarily a web interface\n but can download a binary for linux\n https://espript.ibcp.fr/ESPript/ESPript/esp_faq.php)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/espript.png)\n- [ete](http://etetoolkit.org/gallery/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ete.png)\n- [ggmsa](http://yulab-smu.top/ggmsa/) (See also ggtree)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggmsa.png)\n- [ggtree](https://github.com/YuLab-SMU/ggtree) (see\n https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA\n example)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggtree.png)\n- [Jalview](https://www.jalview.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jalview.jpg)\n- [JSAV](http://www.bioinf.org.uk/software/jsav)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/jsav.png)\n- [MEGA-X](https://www.megasoftware.net/) (original paper from 1994 but actively\n updated. requires EULA for download)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/megax.png)\n- [MSABrowser](https://thekaplanlab.github.io/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/msabrowser.png)\n- [msaR](https://github.com/zachcp/msaR) (uses BioJS/MSA)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/msar.png)\n- [MView](https://www.ebi.ac.uk/Tools/msa/mview/) (See also their web versions\n of clustal omega etc. which have similar outputs)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mview.png)\n- [NCBI MSA Viewer](https://www.ncbi.nlm.nih.gov/projects/msaviewer/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ncbimsa.png)\n- [ProViz](http://slim.icr.ac.uk/proviz/index.php) (See also alphafold\n visualization as tracks\n http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/proviz.png)\n- [pyBoxshade](https://github.com/mdbaron42/pyBoxshade) (also see boxshade)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pyboxshade.png)\n- [pymsaplotter](https://github.com/orangeSi/pymsaploter)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pymsaplotter.png)\n- [React MSAViewer](https://github.com/plotly/react-msa-viewer) (Plotly fully\n deleted the github unfortunately)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/react-msa-viewer.png)\n- [react-msaview](https://github.com/GMOD/react-msaview)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/react-msaview.png)\n- [rMSA](https://github.com/mhahsler/rMSA/blob/master/vignettes/rMSA_vignette.pdf)\n (Can automate boxshade)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rmsa.png)\n- [salti](https://github.com/Sam-Sims/salti)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/salti.png)\n- [Seaview](http://doua.prabi.fr/software/seaview)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seaview.png)\n- [seqotron](https://github.com/4ment/seqotron)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqotron.png)\n- [SeqTUI](https://github.com/ranwez-search/SeqTUI)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqtui.png)\n- [seqvisr](https://github.com/vragh/seqvisr/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqvisr.png)\n- [SNIPViz](http://www.yeastrc.org/snipviz/4.HTML_Config_retrieve_newick_and_fasta_from_server/snip_viz_HTML_config_with_newick_clustering.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpviz.png)\n- [STRAP](http://www.bioinformatics.org/strap/) (also see AA)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/strap.png)\n- [termal](https://github.com/sib-swiss/termal)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/termal.png)\n- [TeXShade](http://mirrors.ibiblio.org/CTAN/macros/latex/contrib/texshade/texshade.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/texshade.png)\n- [Wasabi](http://wasabiapp.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wasabi.png)\n\n## Multi-way synteny\n\n- [hoodini](https://github.com/pentamorfico/hoodini) (Has a number of related\n repos for use in colab)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hoodini.png)\n- [MCGV](https://www.ncbi.nlm.nih.gov/mcgv/cm/mcgv/help)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mcgv.png)\n- [Mumemto](https://github.com/vikshiv/mumemto)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mumemto.png)\n- [SVbyEye](https://htmlpreview.github.io/?https://github.com/daewoooo/SVbyEye/blob/master/man/doc/SVbyEye.html)\n (AKA plotAVA)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svbyeye.png)\n\n## Nanopore\n\n- [CurrentView](https://github.com/genometechlab/currentview) (Visualize and\n compare nanopore ionic current signals from POD5 files aligned to a reference\n via BAM. Overlay conditions, run statistics, GMM fitting, and UMAP, with an\n optional Dash web app.)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/currentview.png)\n\n## Pangenome\n\n- [Pan-Tetris](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pantetris.png)\n- [PanAbyss](https://github.com/Pange31/PanAbyss) (Exploring and visualizing\n large pangenome graphs with PanAbyss: search by coordinates or annotations,\n identify regions shared by individuals or populations, and access other\n interactive features. Uses cytoscape.js)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panabyss.png)\n- [Panacaea](https://github.com/JCVenterInstitute/PanACEA)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panacaea.png)\n- [Panache](https://github.com/SouthGreenPlatform/panache)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panache.png)\n- [panX](http://pangenome.tuebingen.mpg.de/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panx.jpeg)\n- [PGAP-X](https://pgapx.zhaopage.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgapx.png)\n- [PGV (pangenome tool)](https://github.com/ucrbioinfo/PGV)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pgv1.png)\n- [Phandango](https://jameshadfield.github.io/phandango/#/examples)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/phandango.png)\n- [RPAN (3kricedb)](http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rpan.png)\n- [TASUKE](https://tasuke-wiki.dna.naro.go.jp/) (Visualization of multiple\n genomes resequencing data from species having larger genome. Requires a LAMP\n server )\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tasuke.png)\n\n## Phylogenetics\n\n- [Gingr](https://harvest.readthedocs.io/en/latest/content/gingr.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gingr.png)\n- [Nextclade](https://clades.nextstrain.org/) (Related usage on nextstrain app\n also)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nextclade.png)\n- [Taxonium](https://taxonium.org) (Genome variation visualisation in Taxonium\n is provided by the 'Treenome Viewer':\n https://academic.oup.com/bioinformatics/article/39/1/btac772/6858450)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/taxonium.png)\n\n## Population\n\n- [GWAS catalog browser](https://www.ebi.ac.uk/gwas/variants/rs1558902)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gwascatalog.png)\n- [Haploview](https://www.broadinstitute.org/haploview/haploview)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/haploview.png)\n- [Human genome dating](https://human.genome.dating/region/chr1_13250000) (made\n with vega/d3)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/human_genome_dating.png)\n- [Panoptes](https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/panoptes.png)\n- [pixy](https://pixy.readthedocs.io/en/latest/plotting.html#a-genome-wide-plot-of-summary-statistics)\n (The link in readthedocs shows a nice general purpose way to plot\n multi-chromosome plots in ggplot2 with facet grid. Alternative methods for\n multi-chromosome plots shown by the manhattan ggplot2 tutorial\n (https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/ uses\n cumulative bp instead of facet_grid))\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pixy.png)\n- [PopSV](https://github.com/jmonlong/PopSV/blob/master/3-Visualization.md)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/popsv.png)\n- [SWAV](http://swav.popgenetics.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/swav.png)\n- [vcfR](https://knausb.github.io/vcfR_documentation/) (image shows chromoqc\n output)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcfr.png)\n\n## Protein\n\n- [Aquaria](http://aquaria.ws/Q9HD67/5i0i/A)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aquaria.png)\n- [drawProteins](https://github.com/brennanpincardiff/drawProteins)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/drawprotein.png)\n- [Genomics 2 Proteins Portal](https://g2p.broadinstitute.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/g2pportal.png)\n- [IBS (Illustrator for Biological Sequences)](http://ibs.biocuckoo.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ibs.jpg)\n- [nightingale protvista](https://ebi-webcomponents.github.io/nightingale/#/msa)\n (Used on InterProScan website https://www.ebi.ac.uk/interpro/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nightingale.png)\n- [PFAM generate_graphic](https://pfam.xfam.org/generate_graphic) (Also see\n guide here https://pfam.xfam.org/help#tabview=tab10)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pfam.png)\n- [Prosite MyDomains](https://prosite.expasy.org/mydomains)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/prosite.png)\n- [Protael](http://sanshu.github.io/protaelweb/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/protael.png)\n- [ProteinPaint](https://pecan.stjude.cloud/proteinpaint)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/proteinpaint.png)\n- [pViz](https://github.com/Genentech/pviz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pviz.jpg)\n- [TogoStanza Protein Browser](https://db-dev.jpostdb.org/ts/stanza/protein_browser/help.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/togostanza.png)\n\n## Quantitative\n\n- [wasm bigwig demo browser](https://shk656461.github.io/index.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wasm_bigwig.png)\n\n## Repeats\n\n- [GraphAlignmentViewer](https://github.com/Illumina/GraphAlignmentViewer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/graphalignmentviewer.png)\n- [REPAVER](https://gitlab.com/gringer/bioinfscripts/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/repaver.jpg)\n- [REViewer](https://github.com/Illumina/REViewer) (See also\n GraphAlignmentViewer, similar look and from illumina also)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/reviewer.png)\n- [SODA](https://sodaviz.org/) (Describes itself as a low-level library to\n create larger applications with)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/soda.png)\n- [StainedGlass](https://github.com/mrvollger/StainedGlass)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/stainedglass.png)\n- [TRVZ (TRGT tandem repeat genotyping visualizer)](https://github.com/PacificBiosciences/trgt)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trvz.png)\n\n## Sanger\n\n- [ab1lens](https://fishka.bio/ab1lens) (Free, browser-based Sanger / .ab1\n chromatogram viewer. View and compare raw vs analyzed traces and basecalls,\n align a read to a reference to find mismatches, and export a high-resolution\n image. Runs entirely client-side — data never leaves the browser.)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ab1lens.jpg)\n\n## Single cell\n\n- [ArchR](https://www.archrproject.com/articles/Articles/tutorial.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/archr.png)\n- [casper](https://github.com/akdess/CaSpER)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/casper.png)\n- [copykat](https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/copykat.png)\n- [gingko](https://github.com/robertaboukhalil/ginkgo)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gingko.jpeg)\n- [Millefy](https://github.com/yuifu/millefy)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/millefy.png)\n- [MosaicCatcher pipeline](https://github.com/friendsofstrandseq/mosaicatcher-pipeline)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mosaicatcher.png)\n- [numbat](https://kharchenkolab.github.io/numbat/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/numbat.png)\n- [scCNV_heatmap](https://github.com/StefanKurtenbach/scCNV_heatmap)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sccnv_heatmap.png)\n- [vitessce](https://vitessce.io/) (Uses higlass, web based with (optional)\n Python and R integrations, not all visualization are 'genome coordinates')\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vitessce.png)\n\n## Special-purpose\n\n- [SEQing](https://github.com/malewins/SEQing)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqing.png)\n- [UGENE](http://ugene.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ugene.png)\n\n## Splicing\n\n- [IsoVis](https://isomix.org/isovis/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/isovis.png)\n- [Slinker](https://github.com/Oshlack/Slinker) (See also, clinker (gene fusion\n software))\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/slinker.png)\n- [splicejam](https://github.com/jmw86069/splicejam)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/splicejam.png)\n- [Vials](http://vials.io/)\n\n## Static\n\n- [BAMSnap](https://github.com/parklab/bamsnap)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamsnap.png)\n- [bcftools roh](https://samtools.github.io/bcftools/howtos/roh-calling.html)\n (Plots runs of homozygosity, has interactive plot-roh.py helper too)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bcftools_roh.png)\n- [cgplot](https://github.com/dfguan/cgplot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cgplot.png)\n- [ChIA-Pipe](https://github.com/TheJacksonLaboratory/ChIA-PIPE)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chiapipe.png)\n- [CNView](https://github.com/RCollins13/CNView)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnview.jpg)\n- [CNVPlot](https://github.com/dantaki/CNVplot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvplot.jpg)\n- [CNVpytor](https://github.com/abyzovlab/CNVpytor)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/cnvpytor.png)\n- [DNAPlotLib](https://github.com/VoigtLab/dnaplotlib)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/dnaplotlib.png)\n- [ExonIntron](http://wormweb.org/exonintron)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/exonintron.png)\n- [FeatureViewer](https://github.com/calipho-sib/feature-viewer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/featureviewer.png)\n- [geneviewer](https://nvelden.github.io/geneviewer/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneviewer.png)\n- [Geneviz](https://jrderuiter.github.io/geneviz/usage.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/geneviz.png)\n- [Genome STRiP](http://software.broadinstitute.org/software/genomestrip/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomestrip.png)\n- [GenomeTools](http://genometools.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genometools.png)\n- [GenomeView](https://github.com/nspies/genomeview)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeview.png)\n- [genoPlotR](http://genoplotr.r-forge.r-project.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genoplotr.png)\n- [ggbio](http://www.bioconductor.org/packages/2.11/bioc/vignettes/ggbio/inst/doc/ggbio.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggbio.png)\n- [GGgenes](https://github.com/wilkox/gggenes)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gggenes.png)\n- [GGsashimi](https://github.com/guigolab/ggsashimi)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggsashimi.png)\n- [gtrellis](http://bioconductor.org/packages/devel/bioc/vignettes/gtrellis/inst/doc/gtrellis.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gtrellis.png)\n- [Gviz](https://bioconductor.org/packages/release/bioc/html/Gviz.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gviz.png)\n- [Hagfish](https://github.com/mfiers/hagfish/wiki/Plots)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hagfish.png)\n- [HiCPlotter](https://github.com/kcakdemir/HiCPlotter)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hicplotter.jpg)\n- [JVarKit BamToSVG](http://lindenb.github.io/jvarkit/BamToSVG.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bamtosvg.jpg)\n- [Lollipops](https://github.com/joiningdata/lollipops)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/lollipops.png)\n- [Mason](http://www.yeastrc.org/mason/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mason.png)\n- [Methplotlib](https://github.com/wdecoster/methplotlib)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/methplotlib.jpg)\n- [mummer2circos](https://github.com/metagenlab/mummer2circos)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/mummer2circos.png)\n- [Pairoscope](http://pairoscope.sourceforge.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pairoscope.png)\n- [pauvre](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991124/figure/fig-3/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pauvre.png)\n- [pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks) (See also\n https://pypi.org/project/gtracks/ which is a separate project that is powered\n by pyGenomeTracks)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pygenometracks.png)\n- [RACER](https://oliviasabik.github.io/RACERweb/articles/IntroToRACER.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/racer.png)\n- [RepViz](https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4473-z)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/repviz.png)\n- [Samplot](https://github.com/ryanlayer/samplot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/samplot.jpg)\n- [SashimiPlot](https://miso.readthedocs.io/en/fastmiso/sashimi.html) (See also\n rmats2sashimiplot which uses MISO. MATS stands for Multivariate Analysis of\n Transcript Splicing)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sashimi-plot-example.png)\n- [shabam](https://github.com/dlrice/shabam)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/shabam.png)\n- [SparK](https://github.com/harbourlab/SparK)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/spark.png)\n- [Spliceclust](https://github.com/pkimes/spliceclust)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/spliceclust.png)\n- [Sushi](https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/sushi.png)\n- [svist4get](https://link.springer.com/article/10.1186/s12859-019-2706-8)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svis4get.png)\n- [svv](https://github.com/ryanlayer/svv)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svv.png)\n- [svviz](https://github.com/svviz/svviz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svviz.png)\n- [svviz2](https://github.com/nspies/svviz2)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svviz2.png)\n- [trackViewer](https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/trackviewer.png)\n\n## SV\n\n- [AmpliconArchitect](https://github.com/virajbdeshpande/AmpliconArchitect) (The\n term amplicon refers essentially to extrachromosomal DNA in cancer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ampliconarchitect.png)\n- [asgart](https://github.com/delehef/asgart)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/asgart.png)\n- [bigly](https://github.com/brentp/bigly)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/bigly.png)\n- [gGnomes](https://github.com/mskilab/gGnome)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggnomesr.png)\n- [gGnomes.js](https://github.com/mskilab/gGnome.js)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ggnomes.png)\n- [Gremlin](http://compbio.cs.brown.edu/projects/gremlin/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/gremlin.png)\n- [InGAP-SV](http://ingap.sourceforge.net/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/ingap_sv.png)\n- [Introgression browser](https://git.wageningenur.nl/aflit001/ibrowser)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/introgression_browser.png)\n- [NeoLoopFinder](https://github.com/XiaoTaoWang/NeoLoopFinder)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/neoloopfinder.png)\n- [ReConPlot](https://github.com/cortes-ciriano-lab/ReConPlot)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/reconplot.png)\n- [Ribbon](http://genomeribbon.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/genomeribbon.png)\n- [SMRT View](http://files.pacb.com/software/smrtanalysis/2.3.0/doc/smrtview/help/Webhelp/App_View_Epipro.htm)\n (wiki page https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/smrtview.png)\n- [SplitThreader](http://splitthreader.com/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/splitthreader.png)\n- [SVhawkeye](https://github.com/yywan0913/SVhawkeye)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svhawkeye.jpg)\n- [SVPV](https://github.com/VCCRI/SVPV)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svpv.jpg)\n- [SVTopo](https://github.com/PacificBiosciences/SVTopo)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svtopo.png)\n- [vcf2circos](https://github.com/bioinfo-chru-strasbourg/vcf2circos) (Based on\n PCircos https://github.com/CJinny/PCircos)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcf2circos.png)\n\n## Synthetic biology\n\n- [ApE (a plasmid editor)](https://jorgensen.biology.utah.edu/wayned/ape/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/aplasmideditor.png)\n- [Chopchop](http://chopchop.cbu.uib.no/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/chopchop.png)\n- [OpenVectorEditor](https://teselagen.github.io/tg-oss/ove/#/Editor)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/openvectoreditor.png)\n- [plascad](https://github.com/David-OConnor/plascad)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plascad.png)\n- [plasmapR](https://github.com/BradyAJohnston/plasmapR)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plasmapr.png)\n- [seqviz](https://github.com/Lattice-Automation/seqviz#viewer)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqviz.png)\n- [VectorBee](https://www.vectorbee.com/en/) (Not open source, but is free)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vectorbee.png)\n\n## Text-based\n\n- [Alan](https://github.com/mpdunne/alan)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alan.png)\n- [Alv](https://github.com/arvestad/alv)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/alv.png)\n- [ASCIIGenome](https://github.com/dariober/ASCIIGenome)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/asciigenome.png)\n- [BLAST+ (reading -outfmt 0 pairwise output is the original CLI bioinformatics!)](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)\n- [Hapviz](https://github.com/ekg/hapviz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hapviz.png)\n- [pileuppy](https://gitlab.com/tprodanov/pileuppy)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/pileuppy.png)\n- [plotReads](http://campuspress.yale.edu/knightlab/ruddle/plotreads/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/plotreads.png)\n- [rich-msa](https://github.com/althonos/rich-msa)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/richmsa.png)\n- [Rna Alignment Viewers (Colorstock, SScolor, Ratón)](http://biowiki.org/wiki/index.php?title=Rna_Alignment_Viewers\u0026redirect=no)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/rnaalignment.png)\n- [Sam2pairwise](https://github.com/mlafave/sam2pairwise)\n- [Samtools coverage](http://www.htslib.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/samtools_coverage.png)\n- [Samtools depth visualization](https://twitter.com/yokofakun/status/1178686978541441025)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/depthplot.png)\n- [Samtools tview](http://www.htslib.org/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tview.png)\n- [SeqSizzle](https://github.com/ChangqingW/SeqSizzle)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/seqsizzle.png)\n- [SvABA](https://github.com/walaj/svaba#alignmentstxtgz)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/svaba.png)\n- [tgv (terminal genome viewer)](https://github.com/zeqianli/tgv/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tgv.png)\n- [VizAln (from HipSTR)](https://github.com/tfwillems/HipSTR)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/hipstr.png)\n- [wgatools](https://github.com/wjwei-handsome/wgatools)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/wgatools.png)\n\n## Transposons\n\n- [TE-nest](https://github.com/cmdcolin/TEnest) (This was an online tool that\n does not appear to exist anymore see\n https://web.archive.org/web/20170712104431/http://www.plantgdb.org/tool/TEnest/.\n the github link is re-hosted source code also downloaded from archive.org.\n Also note: The notation of nested triangles may be equivalent to just a\n feature being annotated inside a feature: this link helps show this\n https://mcstitzer.github.io/maize_TEs/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/tenest.jpg)\n- [Transposcope](https://github.com/FenyoLab/transposcope)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/transposcope.png)\n\n## Variation\n\n- [NucFreq](https://github.com/mrvollger/NucFreq)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/nucfreq.png)\n- [phasius](https://github.com/wdecoster/phasius)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/phasius.png)\n- [snpit](https://github.com/aineniamh/snipit)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/snpit.png)\n- [vcfPlotein](https://vcfplotein.liigh.unam.mx/#/)\n [(img)](https://cmdcolin.github.io/awesome-genome-visualization/vcfplotein.png)\n\n# Other lists\n\n- [Awesome Bioinformatics](https://github.com/danielecook/Awesome-Bioinformatics)\n- [Genocat](http://genocat.tools/) large collection of genomic visualizations\n with great review paper accompaniment\n https://onlinelibrary.wiley.com/doi/full/10.1111/cgf.13727\n- [awesome-biological-visualizations](https://github.com/keller-mark/awesome-biological-visualizations)\n\nSend in PRs for more stuff!\n\n## License\n\nThis README.md and TOOLS.json are CC0\nhttps://creativecommons.org/publicdomain/zero/1.0/\n\nThe website code is MIT\n","projects_url":"https://awesome.ecosyste.ms/api/v1/lists/cmdcolin%2Fawesome-genome-visualization/projects"}