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viewer"],"name":"Savant","img":"savant.jpg","github":"https://github.com/compbio-UofT/savant","language":["Java"],"url":"http://bioinformatics-ca.github.io/savant_genome_browser_lab_2015/","platform":["Desktop"],"pub":{"url":"https://pubmed.ncbi.nlm.nih.gov/22638571/","doi":"https://doi.org/10.1093/nar/gks427","year":2012,"citations":44},"width":800,"height":561,"github_stars":12},{"tags":["General","Alignments 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viewer"],"name":"Biodalliance","github":"https://github.com/dasmoth/dalliance","url":"http://www.biodalliance.org/","platform":["Web"],"img":"biodalliance.png","pub":{"doi":"http://doi.org/10.1093/bioinformatics/btr020","year":2011,"citations":89},"language":["JS"],"width":2002,"height":766,"github_stars":226},{"tags":["General","Comparative"],"name":"Ensembl genome browser","img":"ensembl.png","pub":{"doi":"https://doi.org/10.1093/nar/30.1.38","year":2002,"citations":1145},"url":"https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237","platform":["Web","Silo"],"width":1121,"height":583},{"tags":["General","Comparative"],"img":"2020ensembl.png","name":"Ensembl genome browser 2020 edition","url":"http://2020.ensembl.org/","platform":["Web"],"width":1378,"height":648},{"tags":["General"],"name":"GBrowse 2","github":"https://github.com/GMOD/GBrowse","img":"gbrowse.png","url":"http://gmod.org/wiki/GBrowse","language":["Perl"],"platform":["Web"],"pub":{"doi":"https://dx.doi.org/10.1093%2Fbib%2Fbbt001","year":2013,"citations":101},"note":"Original gbrowse paper https://doi.org/10.1101/gr.403602","width":800,"height":552,"github_stars":49},{"name":"GenomeMaps","img":"genomemaps.jpg","github":"https://github.com/opencb/genome-maps","url":"http://www.genomemaps.org/","pub":{"url":"https://academic.oup.com/nar/article/41/W1/W41/1113984","doi":"https://doi.org/10.1093/nar/gkt530","year":2013,"citations":25},"tags":["General","Deadlink"],"language":["JS"],"width":489,"height":640,"github_stars":39},{"tags":["General","Epigenomics","Higlass integration","Linear","Circular","Comparative","Quantitative"],"name":"Gosling","img":"gosling.png","github":"https://github.com/gosling-lang/gosling.js","language":["JS","WebGL","Typescript","React"],"platform":["Web"],"url":"https://gosling.js.org/","pub":{"doi":"10.1109/TVCG.2021.3114876","year":2022,"citations":23},"width":1549,"height":777,"github_stars":155},{"tags":["General","Epigenomics","Hi-C"],"name":"HiGlass","img":"higlass.png","github":"https://github.com/higlass/higlass","language":["JS","WebGL"],"pub":{"doi":"10.1186/s13059-018-1486-1","year":2018,"citations":995},"url":"https://higlass.io","platform":["Web","Server"],"width":1250,"height":956,"github_stars":306},{"tags":["General","Alignments viewer"],"name":"IGV.js","language":["JS"],"img":"igvjs.png","pub":{"doi":"https://doi.org/10.1101/2020.05.03.075499","year":2020,"citations":46},"url":"https://github.com/igvteam/igv.js/","platform":["Web"],"width":1116,"height":605,"github_stars":627},{"tags":["General","Alignments viewer","SV","Quantitative","Gene structure"],"name":"JBrowse","note":"See also JBrowse plugin registry https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app using Electron","img":"jbrowse.png","url":"http://jbrowse.org/jbrowse1.html","github":"https://github.com/GMOD/jbrowse","language":["JS"],"platform":["Web","Desktop"],"pub":{"doi":"https://doi.org/10.1186/s13059-016-0924-1","year":2016,"citations":629},"width":2120,"height":1310,"github_stars":459},{"tags":["General","SV","Comparative","Dotplot","Circular","Alignments viewer","Quantitative","Hi-C"],"name":"JBrowse 2","note":"See gallery for more examples https://jbrowse.org/jb2/gallery","img":"jbrowse2.png","github":"https://github.com/GMOD/jbrowse-components","url":"http://jbrowse.org/jb2","language":["JS","Typescript","React"],"pub":{"doi":"https://doi.org/10.1101/2022.07.28.501447","year":2022,"citations":14},"platform":["Web"],"width":1848,"height":1964,"github_stars":192},{"tags":["General","SV","Alignments viewer","Comparative"],"name":"Kero-BROWSE","img":"kerobrowse.png","url":"https://kero.hgc.jp/examples/CLCL/hg38/index.html","github":"https://github.com/DBKERO/genome_browser","platform":["Web"],"pub":{"doi":"https://doi.org/10.1093/nar/gkx1001","year":2017,"citations":44},"language":["JS"],"note":"Also can visualize basic synteny, see tracks e.g. https://kero.hgc.jp/tool/keyword.html#kero:chrX:153,724,868-153,744,762 human vs chimp","width":602,"height":397,"github_stars":7},{"tags":["General","SV","Epigenomics","Gene structure","Splicing"],"name":"NCBI Genome Data Viewer","img":"gdv.png","url":"https://www.ncbi.nlm.nih.gov/genome/gdv/","pub":{"doi":"10.1101/gr.266932.120","year":2020,"citations":104},"platform":["Web","Silo"],"width":1848,"height":697},{"tags":["General"],"name":"Nucleome browser","img":"nucleome.png","url":"https://vis.nucleome.org/v1/main.html","pub":{"doi":"https://doi.org/10.1101/2022.02.21.481225","year":2022,"citations":1},"language":["JS"],"twitter":"https://twitter.com/4DNucleome","note":"github at https://github.com/nucleome","platform":["Web"],"width":1377,"height":471},{"tags":["General","SV"],"name":"Pileup.js","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btw167","year":2016,"citations":18},"img":"pileupjs.png","url":"https://github.com/hammerlab/pileup.js","language":["JS"],"platform":["Web"],"width":1086,"height":597,"github_stars":273},{"tags":["General"],"name":"Trackster","img":"trackster.png","pub":{"doi":"https://doi.org/10.1038/nbt.2404","year":2012,"citations":23},"url":"https://galaxyproject.org/learn/visualization/","platform":["Web"],"width":472,"height":238},{"tags":["General"],"img":"ucsc.jpg","name":"UCSC genome browser","url":"https://genome.ucsc.edu/","github":"https://github.com/ucscGenomeBrowser/kent","pub":{"doi":"10.1101/gr.229102","year":2002,"citations":5618},"platform":["Web","Silo"],"width":512,"height":131,"github_stars":209},{"tags":["General","Quantitative","Epigenomics","Deadlink"],"name":"Valis browser","url":"https://valis.bio/","img":"valis.png","github":"https://github.com/VALIS-software/valis-hpgv","language":["JS","WebGL"],"platform":["Web"],"width":2836,"height":1444,"github_stars":14},{"tags":["General","Epigenomics","Hi-C","Comparative"],"name":"WashU epigenomics browser","github":"https://github.com/lidaof/eg-react","img":"washu.png","url":"https://epigenomegateway.wustl.edu/","pub":{"doi":"https://doi.org/10.1093/nar/gkz348","year":2019,"citations":224},"language":["JS","React"],"note":"The ReactJS is a redesign, there is also a legacy version. Note also, there are comparative features https://www.biorxiv.org/content/10.1101/2022.11.29.518374v1","platform":["Web"],"width":1852,"height":849,"github_stars":65},{"tags":["General"],"name":"Zenbu","img":"zenbu.png","url":"http://fantom.gsc.riken.jp/zenbu/","pub":{"doi":"https://doi.org/10.1038/nbt.2840","year":2014,"citations":143},"platform":["Web"],"width":640,"height":416},{"name":"cgplot","img":"cgplot.png","url":"https://github.com/dfguan/cgplot","language":["Python"],"tags":["Static","Dotplot","Comparative"],"width":3000,"height":3000,"github_stars":9},{"tags":["Dotplot","Comparative"],"name":"D-GENIES","github":"https://github.com/genotoul-bioinfo/dgenies","pub":{"doi":"https://dx.doi.org/10.7717%2Fpeerj.4958","year":2018,"citations":442},"url":"http://dgenies.toulouse.inra.fr/","img":"dgenies.png","language":["JS","Python","D3"],"platform":["Web"],"width":500,"height":500,"github_stars":94},{"tags":["Dotplot","Static","Comparative"],"name":"Delly-maze","img":"maze.png","url":"https://github.com/dellytools/maze","note":"see also https://www.gear-genomics.com/maze/","pub":{"doi":"https://dx.doi.org/10.1093%2Fbioinformatics%2Fbts378","year":2012,"citations":1718},"language":["Python"],"width":2560,"height":1304,"github_stars":9},{"tags":["Dotplot","Static","Comparative"],"name":"Discoplot","img":"discoplot.png","url":"https://github.com/mjsull/DiscoPlot","pub":{"doi":"https://doi.org/10.7287/peerj.preprints.1038v1","year":2015,"citations":0},"language":["Python"],"width":1500,"height":1564,"github_stars":14},{"tags":["Dotplot","Comparative"],"name":"Dot","language":["JS","Python"],"url":"https://dot.sandbox.bio/","github":"https://github.com/MariaNattestad/dot","img":"dot.png","platform":["Web"],"note":"Python data preparation script","width":2500,"height":1324,"github_stars":30},{"tags":["Dotplot"],"name":"Dotlet","img":"dotlet.png","github":"https://github.com/sib-swiss/dotlet","pub":{"doi":"https://doi.org/10.1093/bioinformatics/16.2.178","year":2000,"citations":79},"language":["JS","React"],"platform":["Web"],"url":"https://dotlet.vital-it.ch/","note":"The original publication was 2000 but updated ~2020 with reactjs","width":1377,"height":640,"github_stars":4},{"tags":["Dotplot","Deadlink"],"name":"Dotplot (chirimoyo)","url":"https://chirimoyo.ac.uma.es/bitlab/portfolio/dotplot/","platform":["Web"]},{"tags":["Dotplot"],"name":"iLambda/Dotplot","url":"https://github.com/iLambda/dotplot","platform":["Web"],"github_stars":1},{"tags":["Dotplot","Comparative"],"name":"dotPlotly","url":"https://github.com/tpoorten/dotPlotly/","img":"dotplotly.png","language":["R","Shiny"],"platform":["Web"],"width":700,"height":450,"github_stars":183},{"tags":["Dotplot"],"name":"Dottup","img":"dottup.png","url":"https://www.bioinformatics.nl/cgi-bin/emboss/help/dottup","note":"also seen here http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf","width":539,"height":454},{"tags":["Dotplot"],"name":"FlexiDot","img":"flexidot.png","url":"https://github.com/molbio-dresden/flexidot","pub":{"doi":"https://doi.org/10.1093/bioinformatics/bty395","year":2018,"citations":59},"language":["Python"],"platform":["CLI"],"width":759,"height":564,"github_stars":89},{"tags":["Dotplot","Comparative"],"name":"Gepard","github":"https://github.com/univieCUBE/gepard","url":"http://cube.univie.ac.at/gepard","language":["Java"],"img":"gepard.jpeg","platform":["Desktop"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btm039","year":2007,"citations":579},"width":1088,"height":856,"github_stars":59},{"tags":["Dotplot","Comparative"],"name":"Jdot","url":"https://github.com/LyonsLab/jdot","img":"jdot.png","language":["JS"],"platform":["Web"],"width":689,"height":320,"github_stars":1},{"tags":["Dotplot","Comparative"],"name":"last-dotplot","img":"last_dotplot.png","language":["Python","C++"],"url":"https://gitlab.com/mcfrith/last","platform":["CLI","Web-server"],"width":493,"height":421},{"tags":["Dotplot","Static","Comparative"],"name":"mcutils","img":"mcutils_dotplot.jpeg","language":["R","C++"],"url":"https://github.com/mchaisso/mcutils","note":"https://twitter.com/mjpchaisson/status/1040363992206569472","width":470,"height":404,"github_stars":12},{"tags":["Dotplot","Static","Comparative"],"name":"Minidot","img":"minidot.png","url":"https://github.com/thackl/minidot","language":["R"],"width":1179,"height":683,"github_stars":70},{"tags":["Dotplot","Comparative"],"name":"Mummer-idotplot","url":"https://github.com/ryought/mummer-idotplot","language":["JS","Python"],"platform":["Web","CLI"],"github_stars":25},{"tags":["Dotplot","Static","Comparative"],"name":"Mummerplot","img":"mummerplot.png","github":"https://github.com/mummer4/mummer","url":"http://mummer.sourceforge.net/","pub":{"doi":"10.1186/gb-2004-5-2-r12","year":2004,"citations":4351},"language":["GNUPlot"],"width":3300,"height":2550,"github_stars":426},{"tags":["Dotplot","Comparative"],"img":"mummerplot_ggplot2.png","name":"ggplot2 mummerplot","url":"https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/","language":["R"],"width":1920,"height":1536},{"tags":["Dotplot","Comparative"],"name":"Redotable","img":"redotable.png","url":"https://github.com/s-andrews/redotable","language":["Java"],"platform":["Desktop"],"width":606,"height":585,"github_stars":10},{"tags":["Dotplot","Comparative","Static"],"name":"syntenyPlotByR","img":"synteny_plot_by_r.png","url":"https://github.com/shingocat/syntenyPlotByR","language":["R"],"width":800,"height":800,"github_stars":19},{"tags":["Epigenomics"],"name":"Chip Monk","img":"chipmonk.png","url":"http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/","note":"Also see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/","pub":{"doi":"10.1186/1752-0509-1-S1-P80","year":2007,"citations":3},"language":["Java"],"platform":["Desktop"],"width":800,"height":600},{"tags":["Epigenomics","CNV"],"name":"Chipster","img":"chipster.jpg","github":"https://github.com/chipster/chipster","language":["Java"],"note":"Copy number tutorial https://chipster.csc.fi/manual/cn-tutorial.pdf","url":"https://chipster.csc.fi/","pub":{"doi":"10.1186/1471-2164-12-507","year":2011,"citations":283},"platform":["Desktop"],"width":1201,"height":913,"github_stars":33},{"tags":["Epigenomics"],"name":"cisGenome Browser","img":"cisgenome.png","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btq286","year":2010,"citations":38},"url":"https://jhui2014.github.io/browser/screenshots.html","language":["C"],"platform":["Desktop"],"width":1022,"height":857},{"tags":["Epigenomics","Higlass 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http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage","pub":{"url":"https://academic.oup.com/nar/article/44/W1/W11/2499309","doi":"https://doi.org/10.1093/nar/gkw265","year":2016,"citations":67},"width":1847,"height":925},{"name":"panGraphViewer","url":"https://github.com/TF-Chan-Lab/panGraphViewer","img":"pangraphviewer.jpg","tags":["Graph","Pangenome"],"language":["Python"],"width":479,"height":260,"github_stars":49},{"name":"SVPV","img":"svpv.jpg","language":["Python"],"url":"https://github.com/VCCRI/SVPV","tags":["SV","Coverage"],"pub":{"url":"https://academic.oup.com/bioinformatics/article/33/13/2032/3056003","doi":"https://doi.org/10.1093/bioinformatics/btx117","year":2017,"citations":8},"width":380,"height":597,"github_stars":29},{"name":"wiggleplotr","github":"https://github.com/kauralasoo/wiggleplotr","img":"wiggleplotr.png","url":"http://bioconductor.org/packages/devel/bioc/vignettes/wiggleplotr/inst/doc/wiggleplotr.html","tags":["Coverage"],"language":["R"],"width":576,"height":384,"github_stars":35},{"name":"pretzel","url":"https://github.com/plantinformatics/pretzel","img":"pretzel.png","language":["JS","D3"],"pub":{"doi":"10.1101/517953","year":2019,"citations":20},"tags":["Comparative","Genetic map"],"width":1114,"height":765,"github_stars":42},{"name":"splicejam","language":["R"],"img":"splicejam.png","tags":["Splicing","Sashimi"],"pub":{"doi":"https://doi.org/10.1016/j.celrep.2019.08.093","year":2019,"citations":65},"url":"https://github.com/jmw86069/splicejam","width":384,"height":288,"github_stars":26},{"name":"genomegraphs","language":["R"],"img":"genomegraphs.png","tags":["Ideogram","Quantitative","Splicing"],"url":"http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf","pub":{"doi":"https://doi.org/10.1186/1471-2105-10-2","year":2009,"citations":52},"width":408,"height":775},{"name":"IdeoViz","language":["R"],"img":"ideoviz.png","tags":["Ideogram","Quantitative","Splicing"],"github":"https://github.com/shraddhapai/IdeoViz","url":"https://www.bioconductor.org/packages/release/bioc/vignettes/IdeoViz/inst/doc/Vignette.pdf","width":290,"height":455,"github_stars":1},{"name":"Flash Gviewer","language":["Flash","ActionScript"],"img":"flashgviewer.png","tags":["Ideogram","Genetic map","Historical"],"url":"http://gmod.org/wiki/Flashgviewer/","width":499,"height":806},{"name":"Plotgardener","language":["R"],"img":"plotgardener.png","tags":["Hi-C","Coverage"],"url":"https://github.com/PhanstielLab/plotgardener/","pub":{"doi":"10.1093/bioinformatics/btac057","year":2022,"citations":43},"width":840,"height":510,"github_stars":281},{"name":"MIRA","language":["C++"],"img":"mira.png","tags":["Assembly QC","Alignments viewer","Historical"],"url":"http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html","pub":{"doi":"https://dx.doi.org/10.1101%2Fgr.1917404","year":2004,"citations":869},"note":"orig paper also describes mira here http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf","width":1066,"height":720},{"name":"oxford-plots","url":"https://github.com/jherrero/oxford-plots","img":"oxford.png","tags":["Dotplot"],"language":["R","Perl"],"note":"Has nice description of a synteny pipeline here https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt","width":2000,"height":2000,"github_stars":11},{"name":"IGGE","tags":["Graph","Exotic"],"note":"Not open source","img":"igge.png","url":"https://github.com/immersivegraphgenomeexplorer/IGGE","pub":{"doi":"10.1109/SEGAH52098.2021.9551857","year":2021,"citations":5},"width":247,"height":249,"github_stars":2},{"name":"PipMaker","tags":["Comparative","Repeats","Annotation"],"url":"http://pipmaker.bx.psu.edu/pipmaker/","note":"See also MultiPipMaker http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html","img":"pipmaker.png","pub":{"doi":"https://dx.doi.org/10.1101%2Fgr.10.4.577","year":2000,"citations":892},"width":501,"height":382},{"name":"GraphAlignmentViewer","language":["Python"],"img":"graphalignmentviewer.png","url":"https://github.com/Illumina/GraphAlignmentViewer","tags":["Repeats"],"width":865,"height":755,"github_stars":33},{"name":"MEGA-X","img":"megax.png","language":["Pascal"],"github":"https://github.com/KumarMEGALab/MEGA-source-code","url":"https://www.megasoftware.net/","platform":["Desktop"],"pub":{"doi":"https://doi.org/10.1093/molbev/msab120","year":2021,"citations":7387},"note":"original paper from 1994 but actively updated. requires EULA for download","tags":["MSA","Phylogenetics"],"width":665,"height":450,"github_stars":5},{"name":"Haploview","tags":["Population","Linkage disequilibrium"],"img":"haploview.png","url":"https://www.broadinstitute.org/haploview/haploview","platform":["Desktop"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/bth457","year":2004,"citations":11625},"language":["Java"],"width":800,"height":600},{"name":"AliTreeViz","img":"alitreeviz.png","github":"https://github.com/lipme/alitreeviz","url":"https://www.npmjs.com/package/alitreeviz","tags":["MSA","Phylogenetics"],"language":["JS"],"width":1905,"height":918,"github_stars":4},{"name":"WGDI","img":"wgdi.png","url":"https://github.com/SunPengChuan/wgdi","language":["Python"],"pub":{"doi":"https://doi.org/10.1101/2021.04.29.441969","year":2021,"citations":45},"tags":["Comparative","Dotplot","Circular"],"width":1247,"height":392,"github_stars":106},{"name":"AmpliconArchitect","note":"The term amplicon refers essentially to extrachromosomal DNA in cancer","img":"ampliconarchitect.png","url":"https://github.com/virajbdeshpande/AmpliconArchitect","pub":{"doi":"https://doi.org/10.1038/s41467-018-08200-y","year":2019,"citations":165},"language":["Python"],"tags":["SV","Cancer"],"width":643,"height":323,"github_stars":127},{"name":"PGV (pangenome tool)","img":"pgv1.png","url":"https://github.com/ucrbioinfo/PGV","language":["Python"],"platform":["Web"],"pub":{"url":"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04424-w","doi":"https://doi.org/10.1186/s12859-021-04424-w","year":2021,"citations":4},"tags":["Pangenome","Dotplot","Comparative"],"width":1914,"height":2132,"github_stars":18},{"name":"REViewer","img":"reviewer.png","tags":["Repeats"],"url":"https://github.com/Illumina/REViewer","language":["C++"],"note":"See also GraphAlignmentViewer, similar look and from illumina also","pub":{"doi":"https://doi.org/10.1101/2021.10.20.465046","year":2021,"citations":3},"width":3841,"height":1789,"github_stars":72},{"name":"Trackplot (R)","img":"trackplot.png","url":"https://github.com/PoisonAlien/trackplot","pub":{"doi":"https://doi.org/10.1093/bioadv/vbae031","year":2024,"citations":1},"tags":["Coverage","Gene 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viewer","url":"https://bioinformatics.mdanderson.org/public-software/ideogramviewer/","img":"ideogramviewer.png","language":["JS"],"platform":["Web"],"tags":["Ideogram"],"width":926,"height":394},{"name":"GENESPACE","url":"https://github.com/jtlovell/GENESPACE/","tags":["Comparative","Pangenome"],"img":"genespace.png","pub":{"doi":"https://doi.org/10.7554/eLife.78526","year":2022,"citations":84},"note":"Includes a powerful analysis pipeline, worth reading the paper","language":["R"],"width":730,"height":593,"github_stars":175},{"name":"ggplot2 manhattan plot","url":"https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/","note":"This is not a preconfigured tool but a blog post tutorial with tidy data and ggplot2","img":"ggplot2_manhattan.png","tags":["GWAS"],"language":["R","ggplot2"],"width":2304,"height":960},{"name":"ete","github":"https://github.com/etetoolkit/ete","url":"http://etetoolkit.org/gallery/","language":["Python"],"pub":{"doi":"https://doi.org/10.1093/molbev/msw046","year":2016,"citations":1577},"tags":["MSA","Phylogenetics"],"img":"ete.png","width":640,"height":500,"github_stars":765},{"name":"ggtree","url":"https://github.com/YuLab-SMU/ggtree","language":["R"],"tags":["MSA","Phylogenetics","ggplot2"],"img":"ggtree.png","note":"see https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA example","pub":{"doi":"https://doi.org/10.1111/2041-210X.12628","year":2016,"citations":2905},"width":2100,"height":1050,"github_stars":812},{"name":"Phandango","url":"https://jameshadfield.github.io/phandango/#/examples","github":"https://github.com/jameshadfield/phandango","img":"phandango.png","language":["JS"],"tags":["Pangenome","GWAS","MSA","Phylogenetics","Microbiology"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btx610","year":2017,"citations":402},"width":463,"height":474,"github_stars":111},{"url":"http://athina.biol.uoa.gr/bioinformatics/GENEVITO/","name":"GeneViTo","img":"genevito.jpg","tags":["Microbiology","General"],"pub":{"doi":"https://doi.org/10.1186/1471-2105-4-53","year":2003,"citations":7},"platform":["Desktop"],"language":["Java"],"width":1024,"height":768},{"name":"RegulomeExplorer","url":"http://explorer.cancerregulome.org/all_pairs/?dataset=TCGA_ACC","img":"cancerregulome.png","tags":["Circular","Cancer","SV"],"platform":["Web"],"language":["JS"],"github":"https://github.com/cancerregulome/RegulomeExplorer","width":1852,"height":801,"github_stars":4},{"name":"CGView","tags":["Circular","Microbiology"],"url":"http://cgview.ca/","github":"https://github.com/paulstothard/cgview","pub":{"doi":"https://dx.doi.org/10.1093%2Fnar%2Fgkn179","year":2008,"citations":1065},"platform":["Web"],"language":["JS"],"img":"cgview.png","note":"See also CGView comparison tool and other related https://paulstothard.github.io/cgview_comparison_tool/","width":926,"height":443,"github_stars":37},{"name":"miropeats","img":"miropeats.png","tags":["Comparative","Repeats","Historical"],"language":["Perl","C"],"note":"image from 2021 paper https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf","pub":{"url":"https://academic.oup.com/bioinformatics/article-abstract/11/6/615/187092?redirectedFrom=fulltext","doi":"https://doi.org/10.1093/bioinformatics/11.6.615","year":1995,"citations":36},"url":"http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/","width":654,"height":219},{"name":"Slinker","img":"slinker.png","tags":["Splicing","Coverage"],"language":["Python"],"pub":{"url":"https://f1000research.com/articles/10-1255/v1","doi":"https://doi.org/10.12688/f1000research.74836.1","year":2021,"citations":2},"url":"https://github.com/Oshlack/Slinker","note":"See also, clinker (gene fusion software)","width":819,"height":644,"github_stars":18},{"name":"syntenyPlotteR","img":"syntenyplotter.png","tags":["Comparative"],"url":"https://github.com/marta-fb/syntenyPlotteR","language":["R","ggplot2"],"pub":{"doi":"https://doi.org/10.1093/bioadv/vbad161","year":2023,"citations":3},"width":1440,"height":720,"github_stars":34},{"name":"chromoMap","img":"chromomap.png","tags":["Comparative","Ideogram"],"pub":{"url":"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04556-z","doi":"https://doi.org/10.1186/s12859-021-04556-z","year":2022,"citations":90},"url":"https://lakshay-anand.github.io/chromoMap/index.html","github":"https://github.com/Lakshay-Anand/chromoMap","language":["R"],"width":708,"height":621,"github_stars":3},{"name":"SafFire","img":"saffire.png","tags":["Comparative"],"github":"https://github.com/mrvollger/SafFire","language":["JS"],"url":"https://mrvollger.github.io/SafFire/#ref=CHM13_v1.1&query=GRCh38","width":1776,"height":700,"github_stars":24},{"name":"Gingr","img":"gingr.png","github":"https://github.com/marbl/gingr","language":["C++"],"tags":["Phylogenetics","Comparative","Microbiology"],"pub":{"doi":"https://doi.org/10.1186/s13059-014-0524-x","year":2014,"citations":1225},"url":"https://harvest.readthedocs.io/en/latest/content/gingr.html","width":2551,"height":1558,"github_stars":13},{"name":"StainedGlass","img":"stainedglass.png","language":["R","Python","JS"],"github":"https://github.com/mrvollger/StainedGlass","tags":["Repeats","Heatmap","Higlass 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https://github.com/schneebergerlab/syri","width":1298,"height":863,"github_stars":267},{"name":"seqvisr","img":"seqvisr.png","url":"https://github.com/vragh/seqvisr/","language":["R"],"tags":["MSA","Protein"],"github_stars":9,"width":307,"height":346},{"name":"drawProteins","img":"drawprotein.png","github":"https://github.com/brennanpincardiff/drawProteins","pub":{"doi":"https://doi.org/10.12688/f1000research.14541.1","year":2018,"citations":42},"tags":["Protein"],"language":["R","ggplot2"],"github_stars":33,"width":1649,"height":1933},{"name":"IBS (Illustrator for Biological Sequences)","img":"ibs.jpg","url":"http://ibs.biocuckoo.org/","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btv362","year":2015,"citations":740},"tags":["Protein"],"platform":["Silo","Web","Desktop"],"language":["Java"],"width":800,"height":600},{"name":"PFAM generate_graphic","img":"pfam.png","url":"https://pfam.xfam.org/generate_graphic","note":"Also see guide here https://pfam.xfam.org/help#tabview=tab10","tags":["Protein"],"platform":["Silo","Web"],"width":1370,"height":115},{"name":"SnoopCGH","img":"snoopcgh.jpg","url":"http://snoopcgh.sourceforge.net/","playform":["Desktop"],"tags":["CNV","ArrayCGH"],"language":["Java"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btp488","year":2009,"citations":8},"width":640,"height":388},{"name":"Genovar","img":"genovar.png","tags":["CNV","ArrayCGH","Alignments 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https://sourceforge.net/projects/sybil/","width":687,"height":627},{"name":"SyntenyPortal","img":"syntenyportal.png","language":["JS"],"platform":["Web"],"pub":{"doi":"https://doi.org/10.1093/nar/gkw310","year":2016,"citations":41},"url":"http://bioinfo.konkuk.ac.kr/synteny_portal/","tags":["Comparative","Circular"],"width":1280,"height":647},{"name":"CHROMEISTER","img":"chromeister.png","github":"https://github.com/estebanpw/chromeister","pub":{"doi":"https://doi.org/10.1038/s41598-019-46773-w","year":2019,"citations":25},"tags":["Comparative","Dotplot"],"language":["C","R"],"width":1000,"height":1000,"github_stars":39},{"name":"r2cat","img":"r2cat.jpeg","github":"https://github.com/phuseman/r2cat","pub":{"doi":"https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtp690","year":2009,"citations":105},"tags":["Comparative","Dotplot"],"language":["Java"],"github_stars":3,"width":1800,"height":1598},{"name":"Seaview","img":"seaview.png","language":["C++"],"platform":["Desktop"],"tags":["MSA","Phylogenetics"],"url":"http://doua.prabi.fr/software/seaview","pub":{"doi":"https://doi.org/10.1093/molbev/msp259","year":2009,"citations":4625},"width":927,"height":524},{"name":"SequenceServer","img":"sequenceserver.png","language":["Ruby","JS"],"tags":["BLAST","Comparative","Circular"],"platform":["Web"],"url":"https://sequenceserver.com/","github":"https://github.com/wurmlab/sequenceserver","pub":{"doi":"https://doi.org/10.1093/molbev/msz185","year":2019,"citations":164},"width":1059,"height":355,"github_stars":267},{"name":"numbat","img":"numbat.png","language":["R"],"tags":["Single 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MSAs","img":"cialign.png","language":["Python"],"tags":["MSA"],"pub":{"doi":"https://doi.org/10.7717/peerj.12983","year":2022,"citations":36},"github":"https://github.com/KatyBrown/CIAlign","width":480,"height":286,"github_stars":108},{"name":"CoolBox","img":"coolbox.png","pub":{"doi":"https://doi.org/10.1186/s12859-021-04408-w","year":2021,"citations":19},"github":"https://github.com/GangCaoLab/CoolBox","platform":["CLI","Web"],"tags":["Epigenomics","Hi-C"],"note":"fork of pyGenomeTracks","language":["Python"],"width":760,"height":408,"github_stars":220},{"name":"CNANorm","language":["R"],"url":"https://www.bioconductor.org/packages/release/bioc/html/CNAnorm.html","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btr593","year":2011,"citations":144},"img":"cnanorm.png","tags":["CNV"],"width":436,"height":267},{"name":"GECO","language":["Java"],"tags":["Microbiology","Comparative"],"img":"geco.png","url":"http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet","platform":["Web","Deadlink","No binary or source available"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btl556","year":2006,"citations":21},"width":900,"height":615},{"name":"Orchestral","language":["C++","OpenGL"],"img":"orchestral.png","pub":{"doi":"https://doi.org/10.1109/BioVis.2013.6664351","year":2013,"citations":7},"tags":["CNV","Large display","No binary or source available"],"width":770,"height":355},{"name":"SequenceSurveyor","language":["Adobe 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'Argo'","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btl193","year":2006,"citations":37},"tags":["Comparative"],"language":["Java"],"width":640,"height":253},{"name":"Consed","img":"consed.png","url":"http://bozeman.mbt.washington.edu/consed/consed.html","pub":{"doi":"https://doi.org/10.1101/gr.8.3.195","year":1998,"citations":2677},"tags":["Academic license","Assembly QC","Alignments viewer"],"width":650,"height":994},{"name":"CNSpector","img":"cnspector.png","url":"https://github.com/PapenfussLab/CNspector","pub":{"doi":"https://doi.org/10.1038/s41598-019-42858-8","year":2019,"citations":16},"tags":["CNV"],"width":312,"height":287,"github_stars":4,"language":["R","Shiny"]},{"name":"GenomicBreaks","img":"genomicbreaks.png","url":"https://oist.github.io/GenomicBreaks/articles/GenomicBreaks.html","github":"https://github.com/oist/GenomicBreaks/","language":["R","ggplot2"],"tags":["Comparative","Dotplot"],"width":700,"height":866,"github_stars":4},{"name":"GenomeSyn","img":"genomesyn.png","url":"https://github.com/jmsong2/GenomeSyn","tags":["Comparative","Ideogram","Deadlink"],"language":["Perl"],"platform":["Web","Desktop"],"width":856,"height":522,"github_stars":19},{"name":"CMPlot","img":"cmplot.png","tags":["GWAS"],"language":["R"],"github":"https://github.com/YinLiLin/CMplot","pub":{"doi":"10.1016/j.gpb.2020.10.007","year":2021,"citations":416},"width":525,"height":675,"github_stars":494},{"name":"chromPlot","img":"chromplot.png","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btw137","year":2016,"citations":43},"language":["R"],"tags":["Ideogram","QTL"],"url":"https://www.bioconductor.org/packages/release/bioc/vignettes/chromPlot/inst/doc/chromPlot.pdf","width":440,"height":328},{"name":"PhenoGram","img":"phenogram.png","url":"https://ritchielab.org/software/phenogram-downloads","pub":{"doi":"https://doi.org/10.1186/1756-0381-6-18","year":2013,"citations":172},"note":"Can be web server or download","language":["Ruby"],"platform":["Web","Silo","CLI"],"tags":["Ideogram"],"width":1200,"height":1083},{"name":"RIdeogram","img":"rideogram.png","url":"https://github.com/TickingClock1992/RIdeogram","pub":{"doi":"https://doi.org/10.7717/peerj-cs.251","year":2020,"citations":274},"language":["R"],"tags":["Ideogram","Comparative"],"width":620,"height":646,"github_stars":150},{"name":"CrowsNest","img":"crowsnest.png","tags":["Comparative"],"url":"https://pgsb.helmholtz-muenchen.de/crowsnest/help.html","pub":{"doi":"10.1007/978-1-4939-3167-5_8","year":2016,"citations":1},"width":699,"height":383},{"tags":["Commercial","MSA","SV","Coverage","Alignments 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https://sequenzatools.bitbucket.io/#/home","language":["R"],"tags":["CNV"],"pub":{"doi":"https://doi.org/10.1093/annonc/mdu479","year":2015,"citations":588},"width":960,"height":1056},{"name":"pyCircos","img":"pycircos.png","url":"https://github.com/ponnhide/pyCircos","note":"See also https://github.com/ponnhide/plasmidviewer","width":738,"height":268,"github_stars":317,"tags":["Circular"],"language":["Python"]},{"name":"GeneticsMakie.jl","url":"https://github.com/mmkim1210/GeneticsMakie.jl","img":"geneticsmakie.png","pub":{"doi":"https://doi.org/10.1101/2022.04.18.488573","year":2022,"citations":2},"width":1632,"height":2147,"github_stars":75,"tags":["GWAS","Gene structure","Linkage disequilibrium"],"language":["Julia"]},{"name":"fineSTRUCTURE aka ChromoPainter","img":"finestructure.png","url":"http://www.paintmychromosomes.com/","pub":{"doi":"https://doi.org/10.1371/journal.pgen.1002453","year":2012,"citations":949},"tags":["Local 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See also last-dotplot. Nice figure using it here https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00762-1/figures/4","width":199,"height":713,"github_stars":12},{"name":"GeCoViz","img":"gecoviz.png","url":"https://gecoviz.cgmlab.org/","platform":["Web","Silo"],"tags":["Microbiology","Comparative"],"pub":{"doi":"https://doi.org/10.1093/nar/gkac367","year":2022,"citations":14},"width":472,"height":443},{"name":"GGisy","img":"ggisy.png","url":"https://github.com/Sanrrone/GGisy","language":["Python","R"],"width":544,"height":516,"github_stars":21,"tags":["Comparative","Circular"]},{"name":"multiGenomicContext","url":"https://github.com/Sanrrone/multiGenomicContext","img":"multicontext.png","language":["Python","R"],"width":1145,"height":577,"github_stars":8,"tags":["Comparative"]},{"name":"ggmsa","note":"See also ggtree","url":"http://yulab-smu.top/ggmsa/","github":"https://github.com/YuLab-SMU/ggmsa","pub":{"doi":"https://doi.org/10.1093/bib/bbac222","year":2022,"citations":86},"img":"ggmsa.png","language":["R"],"width":825,"height":188,"github_stars":192,"tags":["MSA"]},{"name":"AccuSyn","language":["JS"],"tags":["Comparative"],"url":"https://accusyn.usask.ca/","github":"https://github.com/jorgenunezsiri/accusyn","img":"accusyn.png","github_stars":16,"width":611,"height":514},{"name":"CView","img":"cview.png","tags":["MSA"],"language":["Java"],"url":"https://sourceforge.net/projects/cview/","pub":{"doi":"https://doi.org/10.1371/journal.pone.0259726","year":2022,"citations":0},"width":1500,"height":802},{"name":"bigly","img":"bigly.png","tags":["SV","Coverage"],"language":["Go","Python"],"url":"https://github.com/brentp/bigly","width":900,"height":500,"github_stars":42},{"name":"signac","img":"signac.png","tags":["Coverage","Single 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https://github.com/ProgrammingLife2017/hygene","language":["Java","Scala"],"width":916,"height":639,"github_stars":1},{"name":"NCBI CGV","img":"cgv.png","tags":["Comparative"],"platform":["Silo"],"url":"https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/05/cgv-beta-release/","width":512,"height":371},{"name":"vcfPlotein","img":"vcfplotein.png","language":["JS","D3","VueJS"],"tags":["Variation"],"url":"https://vcfplotein.liigh.unam.mx/#/","github":"https://github.com/redcpp/vcfplotein","width":1162,"height":254,"github_stars":8},{"name":"CoveragePlotter","img":"coverageplotter.png","language":["Java"],"note":"See also http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html for multi-chromosome","tags":["CNV","Coverage"],"url":"http://lindenb.github.io/jvarkit/CoveragePlotter.html","width":282,"height":109},{"name":"tagore","img":"tagore.png","language":["Python"],"tags":["Ideogram","Local ancestry","Chromosome 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Alternative methods for multi-chromosome plots shown by the manhattan ggplot2 tutorial (https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/ uses cumulative bp instead of facet_grid)","language":["Python","R","ggplot2"],"tags":["Population","Variation"],"doi":{"pub":"https://doi.org/10.1111/1755-0998.13326"},"github_stars":109,"width":1800,"height":900},{"name":"vcf2circos","url":"https://github.com/bioinfo-chru-strasbourg/vcf2circos","img":"vcf2circos.png","note":"Based on PCircos https://github.com/CJinny/PCircos","language":["Python","Plotly"],"tags":["SV","CNV","Circular"],"width":1514,"height":1002,"github_stars":26},{"name":"OmicCircos","tags":["Circular","CNV","Comparative","SV","Coverage"],"language":["R"],"url":"http://bioconductor.org/packages/release/bioc/html/OmicCircos.html","img":"omiccircos.png","pub":{"doi":"10.4137/CIN.S13495","year":2014,"citations":134},"github":"https://github.com/CBIIT-CGBB/OmicCircos2","width":831,"height":1568,"github_stars":5},{"name":"ABrowse (genome browser)","img":"abrowse2.png","tags":["General","Historical"],"language":["JS"],"platform":["Web"],"note":"Had integrations with BioMart, 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pyGenomeTracks","url":"https://gitlab.com/salk-tm/gtracks","img":"gtracks.png","width":1133,"height":297},{"name":"bamscope","tags":["Alignments viewer"],"language":["Kotlin"],"url":"https://github.com/jslfree080/bamscope","img":"bamscope.png","width":1199,"height":1591,"github_stars":9},{"name":"syntR","img":"syntr.png","github":"https://github.com/ksamuk/syntR","url":"https://www.samuklab.com/syntR/articles/syntr_tutorial.html","language":["R"],"tags":["Comparative","Dotplot"],"width":1152,"height":1152,"github_stars":4},{"name":"GCSnap","img":"gcsnap.png","tags":["Comparative"],"github":"https://github.com/JoanaMPereira/GCsnap","pub":{"doi":"https://doi.org/10.1016/j.jmb.2021.166943","year":2021,"citations":8},"language":["Python"],"github_stars":21,"width":4226,"height":1981},{"name":"trackplot (python)","img":"trackplot_python.png","tags":["General","Gene 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viewer"],"name":"Biodalliance","github":"https://github.com/dasmoth/dalliance","url":"http://www.biodalliance.org/","platform":["Web"],"img":"biodalliance.png","pub":{"doi":"http://doi.org/10.1093/bioinformatics/btr020","year":2011,"citations":89},"language":["JS"],"width":2002,"height":766,"github_stars":226},{"tags":["General","Comparative"],"name":"Ensembl genome browser","img":"ensembl.png","pub":{"doi":"https://doi.org/10.1093/nar/30.1.38","year":2002,"citations":1146},"url":"https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237","platform":["Web","Silo"],"width":1121,"height":583},{"tags":["General","Comparative"],"img":"2020ensembl.png","name":"Ensembl genome browser 2020 edition","url":"http://2020.ensembl.org/","platform":["Web"],"width":1378,"height":648},{"tags":["General"],"name":"GBrowse 2","github":"https://github.com/GMOD/GBrowse","img":"gbrowse.png","url":"http://gmod.org/wiki/GBrowse","language":["Perl"],"platform":["Web"],"pub":{"doi":"https://dx.doi.org/10.1093%2Fbib%2Fbbt001","year":2013,"citations":101},"note":"Original gbrowse paper https://doi.org/10.1101/gr.403602","width":800,"height":552,"github_stars":49},{"name":"GenomeMaps","img":"genomemaps.jpg","github":"https://github.com/opencb/genome-maps","url":"http://www.genomemaps.org/","pub":{"url":"https://academic.oup.com/nar/article/41/W1/W41/1113984","doi":"https://doi.org/10.1093/nar/gkt530","year":2013,"citations":25},"tags":["General","Deadlink"],"language":["JS"],"width":489,"height":640,"github_stars":39},{"tags":["General","Epigenomics","Higlass 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viewer"],"name":"IGV.js","language":["JS"],"img":"igvjs.png","pub":{"doi":"https://doi.org/10.1101/2020.05.03.075499","year":2020,"citations":46},"url":"https://github.com/igvteam/igv.js/","platform":["Web"],"width":1116,"height":605,"github_stars":628},{"tags":["General","Alignments viewer","SV","Quantitative","Gene structure"],"name":"JBrowse","note":"See also JBrowse plugin registry https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app using Electron","img":"jbrowse.png","url":"http://jbrowse.org/jbrowse1.html","github":"https://github.com/GMOD/jbrowse","language":["JS"],"platform":["Web","Desktop"],"pub":{"doi":"https://doi.org/10.1186/s13059-016-0924-1","year":2016,"citations":630},"width":2120,"height":1310,"github_stars":459},{"tags":["General","SV","Comparative","Dotplot","Circular","Alignments viewer","Quantitative","Hi-C"],"name":"JBrowse 2","note":"See gallery for more examples https://jbrowse.org/jb2/gallery","img":"jbrowse2.png","github":"https://github.com/GMOD/jbrowse-components","url":"http://jbrowse.org/jb2","language":["JS","Typescript","React"],"pub":{"doi":"https://doi.org/10.1101/2022.07.28.501447","year":2022,"citations":14},"platform":["Web"],"width":1848,"height":1964,"github_stars":192},{"tags":["General","SV","Alignments viewer","Comparative"],"name":"Kero-BROWSE","img":"kerobrowse.png","url":"https://kero.hgc.jp/examples/CLCL/hg38/index.html","github":"https://github.com/DBKERO/genome_browser","platform":["Web"],"pub":{"doi":"https://doi.org/10.1093/nar/gkx1001","year":2017,"citations":44},"language":["JS"],"note":"Also can visualize basic synteny, see tracks e.g. https://kero.hgc.jp/tool/keyword.html#kero:chrX:153,724,868-153,744,762 human vs chimp","width":602,"height":397,"github_stars":7},{"tags":["General","SV","Epigenomics","Gene structure","Splicing"],"name":"NCBI Genome Data Viewer","img":"gdv.png","url":"https://www.ncbi.nlm.nih.gov/genome/gdv/","pub":{"doi":"10.1101/gr.266932.120","year":2020,"citations":106},"platform":["Web","Silo"],"width":1848,"height":697},{"tags":["General"],"name":"Nucleome browser","img":"nucleome.png","url":"https://vis.nucleome.org/v1/main.html","pub":{"doi":"https://doi.org/10.1101/2022.02.21.481225","year":2022,"citations":1},"language":["JS"],"twitter":"https://twitter.com/4DNucleome","note":"github at https://github.com/nucleome","platform":["Web"],"width":1377,"height":471},{"tags":["General","SV"],"name":"Pileup.js","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btw167","year":2016,"citations":18},"img":"pileupjs.png","url":"https://github.com/hammerlab/pileup.js","language":["JS"],"platform":["Web"],"width":1086,"height":597,"github_stars":273},{"tags":["General"],"name":"Trackster","img":"trackster.png","pub":{"doi":"https://doi.org/10.1038/nbt.2404","year":2012,"citations":23},"url":"https://galaxyproject.org/learn/visualization/","platform":["Web"],"width":472,"height":238},{"tags":["General"],"img":"ucsc.jpg","name":"UCSC genome browser","url":"https://genome.ucsc.edu/","github":"https://github.com/ucscGenomeBrowser/kent","pub":{"doi":"10.1101/gr.229102","year":2002,"citations":5634},"platform":["Web","Silo"],"width":512,"height":131,"github_stars":211},{"tags":["General","Quantitative","Epigenomics","Deadlink"],"name":"Valis browser","url":"https://valis.bio/","img":"valis.png","github":"https://github.com/VALIS-software/valis-hpgv","language":["JS","WebGL"],"platform":["Web"],"width":2836,"height":1444,"github_stars":14},{"tags":["General","Epigenomics","Hi-C","Comparative"],"name":"WashU epigenomics browser","github":"https://github.com/lidaof/eg-react","img":"washu.png","url":"https://epigenomegateway.wustl.edu/","pub":{"doi":"https://doi.org/10.1093/nar/gkz348","year":2019,"citations":225},"language":["JS","React"],"note":"The ReactJS is a redesign, there is also a legacy version. Note also, there are comparative features https://www.biorxiv.org/content/10.1101/2022.11.29.518374v1","platform":["Web"],"width":1852,"height":849,"github_stars":66},{"tags":["General"],"name":"Zenbu","img":"zenbu.png","url":"http://fantom.gsc.riken.jp/zenbu/","pub":{"doi":"https://doi.org/10.1038/nbt.2840","year":2014,"citations":143},"platform":["Web"],"width":640,"height":416},{"name":"cgplot","img":"cgplot.png","url":"https://github.com/dfguan/cgplot","language":["Python"],"tags":["Static","Dotplot","Comparative"],"width":3000,"height":3000,"github_stars":9},{"tags":["Dotplot","Comparative"],"name":"D-GENIES","github":"https://github.com/genotoul-bioinfo/dgenies","pub":{"doi":"https://dx.doi.org/10.7717%2Fpeerj.4958","year":2018,"citations":446},"url":"http://dgenies.toulouse.inra.fr/","img":"dgenies.png","language":["JS","Python","D3"],"platform":["Web"],"width":500,"height":500,"github_stars":94},{"tags":["Dotplot","Static","Comparative"],"name":"Delly-maze","img":"maze.png","url":"https://github.com/dellytools/maze","note":"see also https://www.gear-genomics.com/maze/","pub":{"doi":"https://dx.doi.org/10.1093%2Fbioinformatics%2Fbts378","year":2012,"citations":1723},"language":["Python"],"width":2560,"height":1304,"github_stars":9},{"tags":["Dotplot","Static","Comparative"],"name":"Discoplot","img":"discoplot.png","url":"https://github.com/mjsull/DiscoPlot","pub":{"doi":"https://doi.org/10.7287/peerj.preprints.1038v1","year":2015,"citations":0},"language":["Python"],"width":1500,"height":1564,"github_stars":14},{"tags":["Dotplot","Comparative"],"name":"Dot","language":["JS","Python"],"url":"https://dot.sandbox.bio/","github":"https://github.com/MariaNattestad/dot","img":"dot.png","platform":["Web"],"note":"Python data preparation script","width":2500,"height":1324,"github_stars":31},{"tags":["Dotplot"],"name":"Dotlet","img":"dotlet.png","github":"https://github.com/sib-swiss/dotlet","pub":{"doi":"https://doi.org/10.1093/bioinformatics/16.2.178","year":2000,"citations":79},"language":["JS","React"],"platform":["Web"],"url":"https://dotlet.vital-it.ch/","note":"The original publication was 2000 but updated ~2020 with reactjs","width":1377,"height":640,"github_stars":4},{"tags":["Dotplot","Deadlink"],"name":"Dotplot 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http://eichlerlab.gs.washington.edu/pubs/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf","width":539,"height":454},{"tags":["Dotplot"],"name":"FlexiDot","img":"flexidot.png","url":"https://github.com/molbio-dresden/flexidot","pub":{"doi":"https://doi.org/10.1093/bioinformatics/bty395","year":2018,"citations":60},"language":["Python"],"platform":["CLI"],"width":759,"height":564,"github_stars":89},{"tags":["Dotplot","Comparative"],"name":"Gepard","github":"https://github.com/univieCUBE/gepard","url":"http://cube.univie.ac.at/gepard","language":["Java"],"img":"gepard.jpeg","platform":["Desktop"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btm039","year":2007,"citations":580},"width":1088,"height":856,"github_stars":61},{"tags":["Dotplot","Comparative"],"name":"Jdot","url":"https://github.com/LyonsLab/jdot","img":"jdot.png","language":["JS"],"platform":["Web"],"width":689,"height":320,"github_stars":1},{"tags":["Dotplot","Comparative"],"name":"last-dotplot","img":"last_dotplot.png","language":["Python","C++"],"url":"https://gitlab.com/mcfrith/last","platform":["CLI","Web-server"],"width":493,"height":421},{"tags":["Dotplot","Static","Comparative"],"name":"mcutils","img":"mcutils_dotplot.jpeg","language":["R","C++"],"url":"https://github.com/mchaisso/mcutils","note":"https://twitter.com/mjpchaisson/status/1040363992206569472","width":470,"height":404,"github_stars":12},{"tags":["Dotplot","Static","Comparative"],"name":"Minidot","img":"minidot.png","url":"https://github.com/thackl/minidot","language":["R"],"width":1179,"height":683,"github_stars":70},{"tags":["Dotplot","Comparative"],"name":"Mummer-idotplot","url":"https://github.com/ryought/mummer-idotplot","language":["JS","Python"],"platform":["Web","CLI"],"github_stars":25},{"tags":["Dotplot","Static","Comparative"],"name":"Mummerplot","img":"mummerplot.png","github":"https://github.com/mummer4/mummer","url":"http://mummer.sourceforge.net/","pub":{"doi":"10.1186/gb-2004-5-2-r12","year":2004,"citations":4369},"language":["GNUPlot"],"width":3300,"height":2550,"github_stars":429},{"tags":["Dotplot","Comparative"],"img":"mummerplot_ggplot2.png","name":"ggplot2 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https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/","pub":{"doi":"10.1186/1752-0509-1-S1-P80","year":2007,"citations":3},"language":["Java"],"platform":["Desktop"],"width":800,"height":600},{"tags":["Epigenomics","CNV"],"name":"Chipster","img":"chipster.jpg","github":"https://github.com/chipster/chipster","language":["Java"],"note":"Copy number tutorial https://chipster.csc.fi/manual/cn-tutorial.pdf","url":"https://chipster.csc.fi/","pub":{"doi":"10.1186/1471-2164-12-507","year":2011,"citations":283},"platform":["Desktop"],"width":1201,"height":913,"github_stars":33},{"tags":["Epigenomics"],"name":"cisGenome Browser","img":"cisgenome.png","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btq286","year":2010,"citations":38},"url":"https://jhui2014.github.io/browser/screenshots.html","language":["C"],"platform":["Desktop"],"width":1022,"height":857},{"tags":["Epigenomics","Higlass 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usage on nextstrain app also","width":1378,"height":431},{"name":"vcfR","img":"vcfr.png","language":["R"],"tags":["Population","Coverage"],"note":"image shows chromoqc 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http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html","img":"pipmaker.png","pub":{"doi":"https://dx.doi.org/10.1101%2Fgr.10.4.577","year":2000,"citations":892},"width":501,"height":382},{"name":"GraphAlignmentViewer","language":["Python"],"img":"graphalignmentviewer.png","url":"https://github.com/Illumina/GraphAlignmentViewer","tags":["Repeats"],"width":865,"height":755,"github_stars":33},{"name":"MEGA-X","img":"megax.png","language":["Pascal"],"github":"https://github.com/KumarMEGALab/MEGA-source-code","url":"https://www.megasoftware.net/","platform":["Desktop"],"pub":{"doi":"https://doi.org/10.1093/molbev/msab120","year":2021,"citations":7559},"note":"original paper from 1994 but actively updated. requires EULA for download","tags":["MSA","Phylogenetics"],"width":665,"height":450,"github_stars":5},{"name":"Haploview","tags":["Population","Linkage 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ggplot2","img":"ggplot2_manhattan.png","tags":["GWAS"],"language":["R","ggplot2"],"width":2304,"height":960},{"name":"ete","github":"https://github.com/etetoolkit/ete","url":"http://etetoolkit.org/gallery/","language":["Python"],"pub":{"doi":"https://doi.org/10.1093/molbev/msw046","year":2016,"citations":1584},"tags":["MSA","Phylogenetics"],"img":"ete.png","width":640,"height":500,"github_stars":767},{"name":"ggtree","url":"https://github.com/YuLab-SMU/ggtree","language":["R"],"tags":["MSA","Phylogenetics","ggplot2"],"img":"ggtree.png","note":"see https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA example","pub":{"doi":"https://doi.org/10.1111/2041-210X.12628","year":2016,"citations":2928},"width":2100,"height":1050,"github_stars":814},{"name":"Phandango","url":"https://jameshadfield.github.io/phandango/#/examples","github":"https://github.com/jameshadfield/phandango","img":"phandango.png","language":["JS"],"tags":["Pangenome","GWAS","MSA","Phylogenetics","Microbiology"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btx610","year":2017,"citations":403},"width":463,"height":474,"github_stars":113},{"url":"http://athina.biol.uoa.gr/bioinformatics/GENEVITO/","name":"GeneViTo","img":"genevito.jpg","tags":["Microbiology","General"],"pub":{"doi":"https://doi.org/10.1186/1471-2105-4-53","year":2003,"citations":7},"platform":["Desktop"],"language":["Java"],"width":1024,"height":768},{"name":"RegulomeExplorer","url":"http://explorer.cancerregulome.org/all_pairs/?dataset=TCGA_ACC","img":"cancerregulome.png","tags":["Circular","Cancer","SV"],"platform":["Web"],"language":["JS"],"github":"https://github.com/cancerregulome/RegulomeExplorer","width":1852,"height":801,"github_stars":4},{"name":"CGView","tags":["Circular","Microbiology"],"url":"http://cgview.ca/","github":"https://github.com/paulstothard/cgview","pub":{"doi":"https://dx.doi.org/10.1093%2Fnar%2Fgkn179","year":2008,"citations":1073},"platform":["Web"],"language":["JS"],"img":"cgview.png","note":"See also CGView comparison tool and other related https://paulstothard.github.io/cgview_comparison_tool/","width":926,"height":443,"github_stars":37},{"name":"miropeats","img":"miropeats.png","tags":["Comparative","Repeats","Historical"],"language":["Perl","C"],"note":"image from 2021 paper https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf","pub":{"url":"https://academic.oup.com/bioinformatics/article-abstract/11/6/615/187092?redirectedFrom=fulltext","doi":"https://doi.org/10.1093/bioinformatics/11.6.615","year":1995,"citations":36},"url":"http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/","width":654,"height":219},{"name":"Slinker","img":"slinker.png","tags":["Splicing","Coverage"],"language":["Python"],"pub":{"url":"https://f1000research.com/articles/10-1255/v1","doi":"https://doi.org/10.12688/f1000research.74836.1","year":2021,"citations":2},"url":"https://github.com/Oshlack/Slinker","note":"See also, clinker (gene fusion software)","width":819,"height":644,"github_stars":18},{"name":"syntenyPlotteR","img":"syntenyplotter.png","tags":["Comparative"],"url":"https://github.com/marta-fb/syntenyPlotteR","language":["R","ggplot2"],"pub":{"doi":"https://doi.org/10.1093/bioadv/vbad161","year":2023,"citations":3},"width":1440,"height":720,"github_stars":34},{"name":"chromoMap","img":"chromomap.png","tags":["Comparative","Ideogram"],"pub":{"url":"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04556-z","doi":"https://doi.org/10.1186/s12859-021-04556-z","year":2022,"citations":91},"url":"https://lakshay-anand.github.io/chromoMap/index.html","github":"https://github.com/Lakshay-Anand/chromoMap","language":["R"],"width":708,"height":621,"github_stars":3},{"name":"SafFire","img":"saffire.png","tags":["Comparative"],"github":"https://github.com/mrvollger/SafFire","language":["JS"],"url":"https://mrvollger.github.io/SafFire/#ref=CHM13_v1.1&query=GRCh38","width":1776,"height":700,"github_stars":24},{"name":"Gingr","img":"gingr.png","github":"https://github.com/marbl/gingr","language":["C++"],"tags":["Phylogenetics","Comparative","Microbiology"],"pub":{"doi":"https://doi.org/10.1186/s13059-014-0524-x","year":2014,"citations":1232},"url":"https://harvest.readthedocs.io/en/latest/content/gingr.html","width":2551,"height":1558,"github_stars":13},{"name":"StainedGlass","img":"stainedglass.png","language":["R","Python","JS"],"github":"https://github.com/mrvollger/StainedGlass","tags":["Repeats","Heatmap","Higlass integration"],"platform":["Web","CLI"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btac018","year":2022,"citations":51},"width":703,"height":393,"github_stars":91},{"name":"SimpleSynteny","img":"simplesynteny.jpg","url":"https://www.dveltri.com/simplesynteny/about.html","platform":["Web","Server"],"pub":{"doi":"https://doi.org/10.1093/nar/gkw330","year":2016,"citations":97},"tags":["Comparative"],"width":796,"height":277},{"name":"Cinteny","pub":{"doi":"https://doi.org/10.1186/1471-2105-8-82","year":2007,"citations":103},"img":"cinteny.png","tags":["Comparative"],"url":"http://cinteny.cchmc.org/","platform":["Web","Server"],"width":1200,"height":334},{"name":"DAGchainer","url":"http://dagchainer.sourceforge.net/","img":"dagchainer.png","tags":["Dotplot","Comparative"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/bth397","year":2004,"citations":296},"language":["Perl","Java"],"width":813,"height":809},{"name":"AutoGraph","img":"autograph.png","url":"http://autograph.genouest.org/","tags":["Comparative","Deadlink","Historical"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btl618","year":2006,"citations":43},"width":989,"height":1261},{"name":"EvolutionHighway","img":"evolutionaryhighway.jpg","url":"http://eh-demo.ncsa.illinois.edu/","tags":["Comparative","Historical"],"note":"The 'evolutionary highway' image type is reproduced in some other packages e.g. https://github.com/marta-fb/syntenyPlotteR, paper https://doi.org/10.1126/science.1111387","language":["Java","Applet"],"width":715,"height":567},{"name":"Smash++","language":["C++"],"img":"smashpp.png","url":"https://github.com/smortezah/smashpp","pub":{"doi":"https://doi.org/10.1093/gigascience/giaa048","year":2020,"citations":13},"tags":["Comparative"],"width":483,"height":203,"github_stars":56},{"name":"plotsr","img":"plotsr.png","url":"https://github.com/schneebergerlab/plotsr","language":["Python"],"pub":{"doi":"https://doi.org/10.1101/2022.01.24.477489","year":2022,"citations":4},"tags":["Comparative","SV","Pangenome"],"note":"see also https://github.com/schneebergerlab/syri","width":1298,"height":863,"github_stars":267},{"name":"seqvisr","img":"seqvisr.png","url":"https://github.com/vragh/seqvisr/","language":["R"],"tags":["MSA","Protein"],"github_stars":9,"width":307,"height":346},{"name":"drawProteins","img":"drawprotein.png","github":"https://github.com/brennanpincardiff/drawProteins","pub":{"doi":"https://doi.org/10.12688/f1000research.14541.1","year":2018,"citations":43},"tags":["Protein"],"language":["R","ggplot2"],"github_stars":33,"width":1649,"height":1933},{"name":"IBS (Illustrator for Biological Sequences)","img":"ibs.jpg","url":"http://ibs.biocuckoo.org/","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btv362","year":2015,"citations":743},"tags":["Protein"],"platform":["Silo","Web","Desktop"],"language":["Java"],"width":800,"height":600},{"name":"PFAM generate_graphic","img":"pfam.png","url":"https://pfam.xfam.org/generate_graphic","note":"Also see guide here https://pfam.xfam.org/help#tabview=tab10","tags":["Protein"],"platform":["Silo","Web"],"width":1370,"height":115},{"name":"SnoopCGH","img":"snoopcgh.jpg","url":"http://snoopcgh.sourceforge.net/","playform":["Desktop"],"tags":["CNV","ArrayCGH"],"language":["Java"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btp488","year":2009,"citations":8},"width":640,"height":388},{"name":"Genovar","img":"genovar.png","tags":["CNV","ArrayCGH","Alignments 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https://sourceforge.net/projects/sybil/","width":687,"height":627},{"name":"SyntenyPortal","img":"syntenyportal.png","language":["JS"],"platform":["Web"],"pub":{"doi":"https://doi.org/10.1093/nar/gkw310","year":2016,"citations":41},"url":"http://bioinfo.konkuk.ac.kr/synteny_portal/","tags":["Comparative","Circular"],"width":1280,"height":647},{"name":"CHROMEISTER","img":"chromeister.png","github":"https://github.com/estebanpw/chromeister","pub":{"doi":"https://doi.org/10.1038/s41598-019-46773-w","year":2019,"citations":25},"tags":["Comparative","Dotplot"],"language":["C","R"],"width":1000,"height":1000,"github_stars":39},{"name":"r2cat","img":"r2cat.jpeg","github":"https://github.com/phuseman/r2cat","pub":{"doi":"https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtp690","year":2009,"citations":105},"tags":["Comparative","Dotplot"],"language":["Java"],"github_stars":3,"width":1800,"height":1598},{"name":"Seaview","img":"seaview.png","language":["C++"],"platform":["Desktop"],"tags":["MSA","Phylogenetics"],"url":"http://doua.prabi.fr/software/seaview","pub":{"doi":"https://doi.org/10.1093/molbev/msp259","year":2009,"citations":4632},"width":927,"height":524},{"name":"SequenceServer","img":"sequenceserver.png","language":["Ruby","JS"],"tags":["BLAST","Comparative","Circular"],"platform":["Web"],"url":"https://sequenceserver.com/","github":"https://github.com/wurmlab/sequenceserver","pub":{"doi":"https://doi.org/10.1093/molbev/msz185","year":2019,"citations":166},"width":1059,"height":355,"github_stars":267},{"name":"numbat","img":"numbat.png","language":["R"],"tags":["Single 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pyGenomeTracks","language":["Python"],"width":760,"height":408,"github_stars":221},{"name":"CNANorm","language":["R"],"url":"https://www.bioconductor.org/packages/release/bioc/html/CNAnorm.html","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btr593","year":2011,"citations":144},"img":"cnanorm.png","tags":["CNV"],"width":436,"height":267},{"name":"GECO","language":["Java"],"tags":["Microbiology","Comparative"],"img":"geco.png","url":"http://bioinfo.mikrobio.med.uni-giessen.de/geco2/GecoMainServlet","platform":["Web","Deadlink","No binary or source available"],"pub":{"doi":"https://doi.org/10.1093/bioinformatics/btl556","year":2006,"citations":21},"width":900,"height":615},{"name":"Orchestral","language":["C++","OpenGL"],"img":"orchestral.png","pub":{"doi":"https://doi.org/10.1109/BioVis.2013.6664351","year":2013,"citations":7},"tags":["CNV","Large display","No binary or source available"],"width":770,"height":355},{"name":"SequenceSurveyor","language":["Adobe 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'Argo'","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btl193","year":2006,"citations":37},"tags":["Comparative"],"language":["Java"],"width":640,"height":253},{"name":"Consed","img":"consed.png","url":"http://bozeman.mbt.washington.edu/consed/consed.html","pub":{"doi":"https://doi.org/10.1101/gr.8.3.195","year":1998,"citations":2677},"tags":["Academic license","Assembly QC","Alignments 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be web server or download","language":["Ruby"],"platform":["Web","Silo","CLI"],"tags":["Ideogram"],"width":1200,"height":1083},{"name":"RIdeogram","img":"rideogram.png","url":"https://github.com/TickingClock1992/RIdeogram","pub":{"doi":"https://doi.org/10.7717/peerj-cs.251","year":2020,"citations":277},"language":["R"],"tags":["Ideogram","Comparative"],"width":620,"height":646,"github_stars":150},{"name":"CrowsNest","img":"crowsnest.png","tags":["Comparative"],"url":"https://pgsb.helmholtz-muenchen.de/crowsnest/help.html","pub":{"doi":"10.1007/978-1-4939-3167-5_8","year":2016,"citations":1},"width":699,"height":383},{"tags":["Commercial","MSA","SV","Coverage","Alignments 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https://sequenzatools.bitbucket.io/#/home","language":["R"],"tags":["CNV"],"pub":{"doi":"https://doi.org/10.1093/annonc/mdu479","year":2015,"citations":590},"width":960,"height":1056},{"name":"pyCircos","img":"pycircos.png","url":"https://github.com/ponnhide/pyCircos","note":"See also https://github.com/ponnhide/plasmidviewer","width":738,"height":268,"github_stars":318,"tags":["Circular"],"language":["Python"]},{"name":"GeneticsMakie.jl","url":"https://github.com/mmkim1210/GeneticsMakie.jl","img":"geneticsmakie.png","pub":{"doi":"https://doi.org/10.1101/2022.04.18.488573","year":2022,"citations":2},"width":1632,"height":2147,"github_stars":75,"tags":["GWAS","Gene structure","Linkage disequilibrium"],"language":["Julia"]},{"name":"fineSTRUCTURE aka ChromoPainter","img":"finestructure.png","url":"http://www.paintmychromosomes.com/","pub":{"doi":"https://doi.org/10.1371/journal.pgen.1002453","year":2012,"citations":951},"tags":["Local 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See also last-dotplot. Nice figure using it here https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00762-1/figures/4","width":199,"height":713,"github_stars":12},{"name":"GeCoViz","img":"gecoviz.png","url":"https://gecoviz.cgmlab.org/","platform":["Web","Silo"],"tags":["Microbiology","Comparative"],"pub":{"doi":"https://doi.org/10.1093/nar/gkac367","year":2022,"citations":14},"width":472,"height":443},{"name":"GGisy","img":"ggisy.png","url":"https://github.com/Sanrrone/GGisy","language":["Python","R"],"width":544,"height":516,"github_stars":21,"tags":["Comparative","Circular"]},{"name":"multiGenomicContext","url":"https://github.com/Sanrrone/multiGenomicContext","img":"multicontext.png","language":["Python","R"],"width":1145,"height":577,"github_stars":8,"tags":["Comparative"]},{"name":"ggmsa","note":"See also ggtree","url":"http://yulab-smu.top/ggmsa/","github":"https://github.com/YuLab-SMU/ggmsa","pub":{"doi":"https://doi.org/10.1093/bib/bbac222","year":2022,"citations":86},"img":"ggmsa.png","language":["R"],"width":825,"height":188,"github_stars":192,"tags":["MSA"]},{"name":"AccuSyn","language":["JS"],"tags":["Comparative"],"url":"https://accusyn.usask.ca/","github":"https://github.com/jorgenunezsiri/accusyn","img":"accusyn.png","github_stars":16,"width":611,"height":514},{"name":"CView","img":"cview.png","tags":["MSA"],"language":["Java"],"url":"https://sourceforge.net/projects/cview/","pub":{"doi":"https://doi.org/10.1371/journal.pone.0259726","year":2022,"citations":0},"width":1500,"height":802},{"name":"bigly","img":"bigly.png","tags":["SV","Coverage"],"language":["Go","Python"],"url":"https://github.com/brentp/bigly","width":900,"height":500,"github_stars":42},{"name":"signac","img":"signac.png","tags":["Coverage","Single cell"],"url":"https://github.com/timoast/signac/","language":["R"],"pub":{"doi":"https://doi.org/10.1038/s41592-021-01282-5","year":2021,"citations":692},"width":1400,"height":1920,"github_stars":300},{"name":"pyGenomeViz","url":"https://github.com/moshi4/pyGenomeViz","tags":["Comparative"],"language":["Python"],"img":"pygenomeviz.png","width":1291,"height":693,"github_stars":243,"note":"See also https://github.com/moshi4/MGCplotter https://github.com/moshi4/GBKviz https://github.com/moshi4/plot_genome_align_fig"},{"name":"SODA","url":"https://sodaviz.org/","github":"https://github.com/sodaviz/soda","language":["JS","Typescript"],"tags":["Repeats","Circular","Linear"],"img":"soda.png","pub":{"doi":"https://doi.org/10.1093/nargab/lqac077","year":2022,"citations":3},"note":"Describes itself as a low-level library to create larger applications with","width":971,"height":667,"github_stars":6},{"name":"ShinySyn","img":"shinysyn.png","pub":{"doi":"https://doi.org/10.1093/bioinformatics/btac503","year":2022,"citations":11},"tags":["Comparative"],"language":["R","Shiny"],"width":480,"height":808},{"name":"JBR","img":"jbr.png","doi":{"doi":"https://doi.org/10.1093/bioinformatics/btab376"},"tags":["Epigenomics"],"language":["Java"],"note":"Not open source, at least not on github","url":"https://artyomovlab.wustl.edu/jbr/2018_h3k27ac_aging/","github":"https://github.com/Jetbrains-Research/jbr","width":555,"height":283,"github_stars":11},{"name":"clonifier","img":"clonifier.png","github":"https://github.com/dlesl/clonifier","language":["Rust","Typescript","React"],"tags":["Microbiology","Synthetic biology"],"width":555,"height":283,"github_stars":6},{"name":"ctag","img":"ctag.png","github":"https://github.com/AbeelLab/ctag","tags":["Graph","Population"],"note":"See also hygene https://github.com/ProgrammingLife2017/hygene","language":["Java","Scala"],"width":916,"height":639,"github_stars":1},{"name":"NCBI CGV","img":"cgv.png","tags":["Comparative"],"platform":["Silo"],"url":"https://ncbiinsights.ncbi.nlm.nih.gov/2022/07/05/cgv-beta-release/","width":512,"height":371},{"name":"vcfPlotein","img":"vcfplotein.png","language":["JS","D3","VueJS"],"tags":["Variation"],"url":"https://vcfplotein.liigh.unam.mx/#/","github":"https://github.com/redcpp/vcfplotein","width":1162,"height":254,"github_stars":8},{"name":"CoveragePlotter","img":"coverageplotter.png","language":["Java"],"note":"See also http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html for multi-chromosome","tags":["CNV","Coverage"],"url":"http://lindenb.github.io/jvarkit/CoveragePlotter.html","width":282,"height":109},{"name":"tagore","img":"tagore.png","language":["Python"],"tags":["Ideogram","Local ancestry","Chromosome 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way to plot multi-chromosome plots in ggplot2 with facet grid. Alternative methods for multi-chromosome plots shown by the manhattan ggplot2 tutorial (https://danielroelfs.com/blog/how-i-create-manhattan-plots-using-ggplot/ uses cumulative bp instead of facet_grid)","language":["Python","R","ggplot2"],"tags":["Population","Variation"],"doi":{"pub":"https://doi.org/10.1111/1755-0998.13326"},"github_stars":110,"width":1800,"height":900},{"name":"vcf2circos","url":"https://github.com/bioinfo-chru-strasbourg/vcf2circos","img":"vcf2circos.png","note":"Based on PCircos https://github.com/CJinny/PCircos","language":["Python","Plotly"],"tags":["SV","CNV","Circular"],"width":1514,"height":1002,"github_stars":28},{"name":"OmicCircos","tags":["Circular","CNV","Comparative","SV","Coverage"],"language":["R"],"url":"http://bioconductor.org/packages/release/bioc/html/OmicCircos.html","img":"omiccircos.png","pub":{"doi":"10.4137/CIN.S13495","year":2014,"citations":134},"github":"https://github.com/CBIIT-CGBB/OmicCircos2","width":831,"height":1568,"github_stars":6},{"name":"ABrowse (genome browser)","img":"abrowse2.png","tags":["General","Historical"],"language":["JS"],"platform":["Web"],"note":"Had integrations with BioMart, Taverna","pub":{"doi":"10.1186/1471-2105-13-2","year":2012,"citations":17},"width":1200,"height":727},{"name":"VRPG","tags":["Graph","Pangenome"],"img":"vrpg.png","language":["C++","Python"],"platform":["Web"],"url":"https://github.com/codeatcg/VRPG","pub":{"doi":"10.1101/2023.01.20.524991","year":2023,"citations":0},"github_stars":21,"width":949,"height":696},{"name":"Taxonium","note":"Genome variation visualisation in Taxonium is provided by the 'Treenome Viewer': https://academic.oup.com/bioinformatics/article/39/1/btac772/6858450","tags":["Phylogenetics","Microbiology"],"img":"taxonium.png","language":["JS","Python"],"platform":["Web"],"url":"https://taxonium.org","pub":{"doi":"10.7554/eLife.82392","year":2022,"citations":28},"github_stars":86,"width":1000,"height":525},{"name":"MosaicCatcher pipeline","tags":["Single 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pyGenomeTracks","url":"https://gitlab.com/salk-tm/gtracks","img":"gtracks.png","width":1133,"height":297},{"name":"bamscope","tags":["Alignments viewer"],"language":["Kotlin"],"url":"https://github.com/jslfree080/bamscope","img":"bamscope.png","width":1199,"height":1591,"github_stars":9},{"name":"syntR","img":"syntr.png","github":"https://github.com/ksamuk/syntR","url":"https://www.samuklab.com/syntR/articles/syntr_tutorial.html","language":["R"],"tags":["Comparative","Dotplot"],"width":1152,"height":1152,"github_stars":4},{"name":"GCSnap","img":"gcsnap.png","tags":["Comparative"],"github":"https://github.com/JoanaMPereira/GCsnap","pub":{"doi":"https://doi.org/10.1016/j.jmb.2021.166943","year":2021,"citations":8},"language":["Python"],"github_stars":22,"width":4226,"height":1981},{"name":"trackplot (python)","img":"trackplot_python.png","tags":["General","Gene 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paper","width":1000,"height":618,"github_stars":115},{"name":"genoVi","img":"genovi.png","url":"https://github.com/robotoD/GenoVi","language":["Python"],"pub":{"doi":"https://doi.org/10.1371/journal.pcbi.1010998","year":2023,"citations":17},"tags":["Circular","Comparative","Microbiology"],"width":1500,"height":1500,"github_stars":67},{"name":"TRVZ (TRGT tandem repeat genotyping visualizer)","img":"trvz.png","language":["Rust"],"url":"https://github.com/PacificBiosciences/trgt","tags":["Repeats","Graph"],"pub":{"doi":"https://doi.org/10.1101/2023.05.12.540470","year":2023,"citations":10},"width":3154,"height":2261,"github_stars":93},{"name":"BRICK (BRIG-like circular knowledgebase)","note":"See also BRIG","github":"https://github.com/esteinig/brick","url":"https://brick.ink/","img":"brick.png","language":["JS"],"tags":["Circular","Comparative","Microbiology"],"width":1096,"height":836,"github_stars":11},{"name":"SGTK (scaffold graph 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gggenomes","width":5905,"height":2362,"github_stars":61},{"tags":["Static","Comparative"],"name":"geneviewer","img":"geneviewer.png","url":"https://nvelden.github.io/geneviewer/","github":"https://github.com/nvelden/geneviewer","language":["R"],"width":1492,"height":1247,"github_stars":19},{"name":"figeno","img":"figeno.png","tags":["Hi-C","Epigenomics","Methylation","Alignments viewer"],"language":["Python","JS"],"url":"https://github.com/CompEpigen/figeno","pub":{"doi":"https://doi.org/10.1101/2024.04.22.590500 ","year":2024,"citations":1},"width":2882,"height":1197,"github_stars":224},{"name":"SVhawkeye","img":"svhawkeye.jpg","tags":["SV","Alignments 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https://github.com/rraadd88/beditor","width":576,"height":1106,"github_stars":4},{"name":"waragraph","img":"waragraph.png","tags":["Graph"],"url":"https://chfi.github.io/waragraph/","github":"https://github.com/chfi/waragraph","note":"Deployed to the web via wasm","language":["Rust"],"platform":["Web","Desktop"],"width":1783,"height":901,"github_stars":23},{"name":"gff2ps","url":"https://genome.crg.es/software/gfftools/GFF2PS.html","pub":{"doi":"10.1093/bioinformatics/16.8.743","year":2000,"citations":40},"img":"gff2ps.png","tags":["Historical"],"note":"Used to make original figures for the human Celera genome","width":1114,"height":985},{"name":"SVbyEye","img":"svbyeye.png","github":"https://github.com/daewoooo/SVbyEye/","url":"https://htmlpreview.github.io/?https://github.com/daewoooo/SVbyEye/blob/master/vignettes/SVbyEye.html","tags":["Multi-way synteny","Comparative"],"language":["R"],"width":1455,"height":903,"github_stars":17}]}]}]