TOOLS.json

{
  "tools": [
    {
      "tags": ["Commercial"],
      "name": "10x genomics/Loupe",
      "url": "https://support.10xgenomics.com/genome-exome/software/visualization/latest/structural-variants",
      "img": "10xgenomics.png",
      "interactive": ["true"],
      "width": 1600,
      "height": 300
    },
    {
      "tags": ["Commercial"],
      "name": "Alamut",
      "img": "alamut.png",
      "url": "https://www.interactive-biosoftware.com/alamut-visual/",
      "interactive": ["true"],
      "width": 938,
      "height": 132
    },
    {
      "tags": ["Commercial", "Microbiology"],
      "name": "ATCC Genome Portal",
      "platform": ["Silo"],
      "img": "atcc.png",
      "url": "https://docs.onecodex.com/en/articles/3996697-using-the-genome-browser",
      "interactive": ["true"],
      "width": 2602,
      "height": 1276
    },
    {
      "tags": ["Commercial", "Synthetic biology"],
      "name": "Benchling",
      "img": "benchling.png",
      "url": "https://www.benchling.com/",
      "interactive": ["true"],
      "width": 1710,
      "height": 896
    },
    {
      "tags": ["Commercial", "SV"],
      "name": "CLC Genomics workbench",
      "img": "clcgenomics.png",
      "url": "https://digitalinsights.qiagen.com/news/blog/discovery/structural-variant-detection-using-clc-genomics-workbench/",
      "interactive": ["true"],
      "width": 600,
      "height": 455
    },
    {
      "tags": ["Commercial"],
      "name": "DNASTAR",
      "img": "dnastar.png",
      "url": "https://www.dnastar.com/",
      "interactive": ["true"],
      "width": 438,
      "height": 253
    },
    {
      "tags": ["Commercial", "Synthetic biology"],
      "name": "Geneious",
      "img": "geneious.png",
      "url": "https://www.geneious.com/",
      "interactive": ["true"],
      "width": 1000,
      "height": 600
    },
    {
      "tags": ["Commercial"],
      "name": "Genestack",
      "img": "genestack.png",
      "url": "https://genestack.com/blog/2015/05/28/navigation-in-genestack-genome-browser/",
      "interactive": ["true"],
      "width": 1256,
      "height": 556
    },
    {
      "tags": ["Commercial"],
      "name": "Golden Helix",
      "img": "goldenhelix.png",
      "url": "https://www.goldenhelix.com/products/GenomeBrowse/",
      "note": "Free for academic use",
      "interactive": ["true"],
      "width": 360,
      "height": 245
    },
    {
      "tags": ["Commercial"],
      "name": "Lucid viewer",
      "img": "lucidalign.png",
      "url": "https://lucidalign.com/",
      "interactive": ["true"],
      "width": 1024,
      "height": 540
    },
    {
      "tags": ["Commercial"],
      "name": "MacVector",
      "img": "macvector.png",
      "url": "https://macvector.com/",
      "width": 598,
      "height": 478
    },
    {
      "tags": ["Commercial", "Comparative"],
      "name": "Persephone",
      "img": "persephone.jpg",
      "url": "https://persephonesoft.com/",
      "width": 576,
      "height": 313
    },
    {
      "tags": ["Commercial"],
      "img": "snapgene.png",
      "name": "SnapGene",
      "url": "https://www.snapgene.com/",
      "width": 777,
      "height": 436
    },
    {
      "tags": ["Commercial"],
      "img": "strandngs.png",
      "name": "Strand NGS",
      "url": "https://www.strand-ngs.com/",
      "width": 786,
      "height": 478
    },
    {
      "tags": ["Commercial", "SV"],
      "img": "bionano.png",
      "name": "Bionano",
      "url": "https://bionanogenomics.com/technology/structural-variation/",
      "width": 568,
      "height": 295
    },
    {
      "tags": ["MSA"],
      "name": "AA (alignment annotator)",
      "pub": {
        "doi": "10.1093/nar/gku400",
        "year": 2014,
        "citations": 52
      },
      "note": "also see STRAP",
      "img": "aa.png",
      "language": ["JS"],
      "url": "http://www.bioinformatics.org/strap/aa",
      "platform": ["Web"],
      "width": 1222,
      "height": 539
    },
    {
      "tags": ["MSA"],
      "name": "abrowse (MSA viewer)",
      "language": ["JS"],
      "img": "abrowse.png",
      "url": "https://github.com/ihh/abrowse",
      "platform": ["Web"],
      "width": 1848,
      "height": 533,
      "github_stars": 11
    },
    {
      "tags": ["MSA"],
      "name": "alignment.js",
      "img": "alignmentjs.png",
      "url": "https://github.com/veg/alignment.js",
      "language": ["JS"],
      "platform": ["Web"],
      "width": 2006,
      "height": 454,
      "github_stars": 6
    },
    {
      "tags": ["MSA"],
      "name": "AlignmentComparator",
      "img": "alignmentcomparator.png",
      "github": "https://github.com/bioinfweb/AlignmentComparator",
      "url": "http://bioinfweb.info/AlignmentComparator/",
      "note": "Uses http://bioinfweb.info/LibrAlign/",
      "language": ["Java"],
      "width": 756,
      "height": 592,
      "github_stars": 1
    },
    {
      "tags": ["MSA"],
      "name": "AlignmentViewer",
      "img": "alignmentviewer.png",
      "language": ["JS"],
      "github": "https://github.com/sanderlab/alignmentviewer",
      "url": "https://alignmentviewer.org/",
      "pub": {
        "url": "https://f1000research.com/articles/9-213",
        "doi": "https://doi.org/10.12688/f1000research.22242.2",
        "year": 2020,
        "citations": 5
      },
      "platform": ["Web"],
      "width": 1848,
      "height": 716,
      "github_stars": 25
    },
    {
      "tags": ["MSA"],
      "name": "AliView",
      "img": "aliview.png",
      "url": "http://www.ormbunkar.se/aliview/",
      "github": "https://github.com/AliView/AliView",
      "pub": {
        "doi": "10.1093/bioinformatics/btu531",
        "year": 2014,
        "citations": 2260
      },
      "platform": ["Desktop"],
      "language": ["Java"],
      "width": 400,
      "height": 241,
      "github_stars": 108
    },
    {
      "tags": ["MSA"],
      "name": "BioJS/MSA",
      "language": ["JS"],
      "url": "https://msa.biojs.net/",
      "img": "biojsmsa.png",
      "github": "https://github.com/wilzbach/msa",
      "platform": ["Web"],
      "pub": {
        "url": "https://academic.oup.com/bioinformatics/article/32/22/3501/2525598?login=true",
        "doi": "10.1093/bioinformatics/btw474",
        "year": 2016,
        "citations": 147
      },
      "width": 1956,
      "height": 634,
      "github_stars": 167
    },
    {
      "name": "rMSA",
      "url": "https://github.com/mhahsler/rMSA/blob/master/vignettes/rMSA_vignette.pdf",
      "note": "Can automate boxshade",
      "github": "https://github.com/mhahsler/rMSA",
      "img": "rmsa.png",
      "tags": ["MSA"],
      "language": ["R"],
      "width": 650,
      "height": 407,
      "github_stars": 9
    },
    {
      "tags": ["MSA", "Deadlink"],
      "name": "Boxshade",
      "note": "Also available as a command line tool with `apt install boxshade`. See also rMSA which can automate running boxshade from within R",
      "img": "boxshade.png",
      "url": "https://embnet.vital-it.ch/software/BOX_form.html",
      "pub": {
        "url": "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2000-1-2-reports2047",
        "doi": "10.1186/gb-2000-1-2-reports2047",
        "year": 2000,
        "citations": 8
      },
      "platform": ["Web", "CLI"],
      "width": 915,
      "height": 249
    },
    {
      "tags": ["MSA"],
      "name": "ESPript",
      "img": "espript.png",
      "pub": {
        "doi": "10.1093/bioinformatics/15.4.305",
        "year": 1999,
        "citations": 2395
      },
      "url": "http://espript.ibcp.fr/ESPript/ESPript/",
      "platform": ["Web", "CLI"],
      "note": "Primarily a web interface but can download a binary for linux https://espript.ibcp.fr/ESPript/ESPript/esp_faq.php",
      "width": 830,
      "height": 204
    },
    {
      "tags": ["MSA"],
      "name": "Jalview",
      "img": "jalview.jpg",
      "url": "https://www.jalview.org/",
      "pub": {
        "doi": "10.1093/bioinformatics/btp033",
        "year": 2009,
        "citations": 7615
      },
      "platform": ["Desktop"],
      "language": ["Java"],
      "width": 520,
      "height": 377
    },
    {
      "tags": ["MSA"],
      "name": "JSAV",
      "img": "jsav.png",
      "github": "https://github.com/AndrewCRMartin/JSAV",
      "url": "http://www.bioinf.org.uk/software/jsav",
      "language": ["JS"],
      "platform": ["Web"],
      "pub": {
        "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304231/",
        "doi": "10.12688/f1000research.5486.1",
        "year": 2014,
        "citations": 14
      },
      "width": 1000,
      "height": 836,
      "github_stars": 11
    },
    {
      "tags": ["Logo"],
      "name": "LogoJS",
      "img": "logojs.png",
      "github": "https://github.com/weng-lab/logojs-package",
      "language": ["JS"],
      "url": "https://logojs.wenglab.org/app/gallery/",
      "pub": {
        "doi": "10.1093/bioinformatics/btaa192",
        "year": 2020,
        "citations": 8
      },
      "platform": ["Web"],
      "width": 413,
      "height": 254,
      "github_stars": 14
    },
    {
      "tags": ["MSA"],
      "name": "MSABrowser",
      "img": "msabrowser.png",
      "language": ["JS"],
      "github": "https://github.com/thekaplanlab/msabrowser",
      "url": "https://thekaplanlab.github.io/",
      "pub": {
        "doi": "https://doi.org/10.1093/bioadv/vbab009",
        "year": 2021,
        "citations": 2
      },
      "platform": ["Web"],
      "width": 1654,
      "height": 290,
      "github_stars": 30
    },
    {
      "tags": ["MSA"],
      "name": "msaR",
      "url": "https://github.com/zachcp/msaR",
      "img": "msar.png",
      "note": "uses BioJS/MSA",
      "language": ["R", "JS"],
      "platform": ["Desktop", "R/htmlwidget"],
      "width": 1000,
      "height": 580,
      "github_stars": 8
    },
    {
      "tags": ["MSA"],
      "name": "MView",
      "url": "https://www.ebi.ac.uk/Tools/msa/mview/",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/14.4.380",
        "year": 1998,
        "citations": 296
      },
      "img": "mview.png",
      "note": "See also their web versions of clustal omega etc. which have similar outputs",
      "platform": ["Web", "Silo"],
      "width": 1222,
      "height": 550
    },
    {
      "tags": ["MSA"],
      "name": "NCBI MSA Viewer",
      "url": "https://www.ncbi.nlm.nih.gov/projects/msaviewer/",
      "img": "ncbimsa.png",
      "platform": ["Web", "CGI", "Silo"],
      "width": 1222,
      "height": 459
    },
    {
      "tags": ["MSA"],
      "name": "pyBoxshade",
      "img": "pyboxshade.png",
      "url": "https://github.com/mdbaron42/pyBoxshade",
      "language": ["Python"],
      "note": "also see boxshade",
      "platform": ["Desktop"],
      "width": 519,
      "height": 304,
      "github_stars": 22
    },
    {
      "tags": ["MSA"],
      "name": "pymsaplotter",
      "language": ["Python"],
      "img": "pymsaplotter.png",
      "url": "https://github.com/orangeSi/pymsaploter",
      "width": 1000,
      "height": 513,
      "github_stars": 9
    },
    {
      "tags": ["MSA"],
      "name": "React MSAViewer",
      "img": "react-msa-viewer.png",
      "language": ["JS", "React"],
      "url": "https://github.com/plotly/react-msa-viewer",
      "platform": ["Web"],
      "width": 595,
      "height": 243,
      "github_stars": 25
    },
    {
      "tags": ["MSA"],
      "name": "react-msaview",
      "img": "react-msaview.png",
      "language": ["JS", "React"],
      "url": "https://github.com/GMOD/react-msaview",
      "width": 1177,
      "height": 413,
      "github_stars": 14
    },
    {
      "tags": ["MSA"],
      "name": "seqotron",
      "img": "seqotron.png",
      "url": "https://github.com/4ment/seqotron",
      "pub": {
        "doi": "10.1186/s13104-016-1927-4",
        "year": 2016,
        "citations": 35
      },
      "language": ["Objective-C"],
      "platform": ["Desktop"],
      "width": 826,
      "height": 602,
      "github_stars": 28
    },
    {
      "tags": ["MSA"],
      "name": "STRAP",
      "note": "also see AA",
      "img": "strap.png",
      "url": "http://www.bioinformatics.org/strap/",
      "pub": {
        "doi": "10.1093/nar/gku400",
        "year": 2014,
        "citations": 52
      },
      "platform": ["Web", "Applet"],
      "width": 725,
      "height": 380
    },
    {
      "tags": ["MSA"],
      "name": "TeXShade",
      "img": "texshade.png",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/16.2.135",
        "year": 2000,
        "citations": 264
      },
      "url": "http://mirrors.ibiblio.org/CTAN/macros/latex/contrib/texshade/texshade.pdf",
      "platform": ["Desktop"],
      "width": 2872,
      "height": 761
    },
    {
      "tags": ["MSA"],
      "name": "Wasabi",
      "img": "wasabi.png",
      "url": "http://wasabiapp.org/",
      "github": "https://github.com/veidenberg/wasabi",
      "language": ["JS", "Python"],
      "pub": {
        "doi": "https://doi.org/10.1093/molbev/msv333",
        "year": 2015,
        "citations": 51
      },
      "platform": ["Web"],
      "width": 1378,
      "height": 496,
      "github_stars": 16
    },
    {
      "tags": ["CNV", "Static"],
      "name": "aCNVViewer",
      "img": "acnvviewer.png",
      "language": ["Python"],
      "url": "https://github.com/FJD-CEPH/aCNViewer",
      "pub": {
        "url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189334",
        "doi": "https://doi.org/10.1371/journal.pone.0189334",
        "year": 2017,
        "citations": 6
      },
      "width": 4000,
      "height": 1800,
      "github_stars": 27
    },
    {
      "name": "CNVkit",
      "tags": ["CNV"],
      "img": "cnvkit.png",
      "url": "https://cnvkit.readthedocs.io/en/stable/plots.html",
      "github": "https://github.com/etal/cnvkit",
      "language": ["Python"],
      "pub": {
        "url": "https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004873",
        "doi": "https://doi.org/10.1371/journal.pcbi.1004873",
        "year": 2016,
        "citations": 1264
      },
      "width": 885,
      "height": 1555,
      "github_stars": 498
    },
    {
      "tags": ["CNV", "Static"],
      "language": ["C", "R"],
      "name": "BAMScale",
      "img": "bamscale.png",
      "url": "https://github.com/ncbi/BAMscale",
      "pub": {
        "url": "https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-020-00343-x",
        "doi": "10.1186/s13072-020-00343-x",
        "year": 2020,
        "citations": 42
      },
      "width": 2172,
      "height": 498,
      "github_stars": 63
    },
    {
      "tags": ["Static", "Alignments viewer"],
      "language": ["Python"],
      "img": "bamsnap.png",
      "name": "BAMSnap",
      "url": "https://github.com/parklab/bamsnap",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btaa1101",
        "year": 2021,
        "citations": 7
      },
      "width": 1000,
      "height": 1121,
      "github_stars": 107
    },
    {
      "tags": ["Static", "Epigenomics"],
      "name": "ChIA-Pipe",
      "img": "chiapipe.png",
      "url": "https://github.com/TheJacksonLaboratory/ChIA-PIPE",
      "pub": {
        "url": "https://www.science.org/doi/10.1126/sciadv.aay2078",
        "doi": "10.1126/sciadv.aay2078",
        "year": 2020,
        "citations": 23
      },
      "width": 541,
      "height": 562,
      "github_stars": 26
    },
    {
      "tags": ["Gene fusion", "Circular", "Linear"],
      "name": "Chimeraviz",
      "img": "chimeraviz.png",
      "url": "https://github.com/stianlagstad/chimeraviz",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btx329",
        "year": 2017,
        "citations": 23
      },
      "language": ["R"],
      "width": 1914,
      "height": 1935,
      "github_stars": 36
    },
    {
      "tags": ["Static", "CNV"],
      "name": "CNView",
      "img": "cnview.jpg",
      "url": "https://github.com/RCollins13/CNView",
      "pub": {
        "doi": "https://doi.org/10.1101/049536",
        "year": 2016,
        "citations": 10
      },
      "language": ["R"],
      "width": 1260,
      "height": 900,
      "github_stars": 68
    },
    {
      "tags": ["Static", "CNV"],
      "name": "CNVPlot",
      "img": "cnvplot.jpg",
      "url": "https://github.com/dantaki/CNVplot",
      "pub": {
        "doi": "10.1101/030270",
        "year": 2015,
        "citations": 0
      },
      "language": ["R"],
      "width": 535,
      "height": 537,
      "github_stars": 15
    },
    {
      "tags": ["Static", "CNV"],
      "name": "CNVpytor",
      "img": "cnvpytor.png",
      "url": "https://github.com/abyzovlab/CNVpytor",
      "pub": {
        "doi": "https://doi.org/10.1093/gigascience/giab074",
        "year": 2021,
        "citations": 41
      },
      "language": ["Python"],
      "width": 1024,
      "height": 1024,
      "github_stars": 163
    },
    {
      "tags": ["Static", "Synthetic biology"],
      "name": "DNAPlotLib",
      "img": "dnaplotlib.png",
      "url": "https://github.com/VoigtLab/dnaplotlib",
      "pub": {
        "doi": "10.1021/acssynbio.6b00252",
        "year": 2016,
        "citations": 48
      },
      "language": ["Python"],
      "width": 960,
      "height": 810,
      "github_stars": 286
    },
    {
      "name": "ExonIntron",
      "url": "http://wormweb.org/exonintron",
      "img": "exonintron.png",
      "tags": ["Static", "Gene structure"],
      "width": 387,
      "height": 78
    },
    {
      "tags": ["Static", "Gene structure"],
      "name": "FeatureViewer",
      "img": "featureviewer.png",
      "pub": {
        "doi": "https://doi.org/10.5281/zenodo.596941"
      },
      "url": "https://github.com/calipho-sib/feature-viewer",
      "platform": ["Web"],
      "width": 2736,
      "height": 970,
      "github_stars": 107
    },
    {
      "tags": ["Static", "Gene structure"],
      "name": "Geneviz",
      "img": "geneviz.png",
      "url": "https://jrderuiter.github.io/geneviz/usage.html",
      "github": "https://github.com/jrderuiter/geneviz",
      "language": ["Python"],
      "width": 640,
      "height": 152,
      "github_stars": 15
    },
    {
      "tags": ["Static"],
      "name": "Genome STRiP",
      "img": "genomestrip.png",
      "pub": {
        "doi": "10.1038/ng.3200",
        "year": 2015,
        "citations": 349
      },
      "url": "http://software.broadinstitute.org/software/genomestrip/",
      "width": 1133,
      "height": 466
    },
    {
      "tags": ["Static", "Gene structure"],
      "name": "GenomeTools",
      "img": "genometools.png",
      "github": "https://github.com/genometools/genometools",
      "url": "http://genometools.org/",
      "pub": {
        "doi": "10.1109/TCBB.2013.68",
        "year": 2013,
        "citations": 336
      },
      "language": ["C"],
      "width": 700,
      "height": 326,
      "github_stars": 281
    },
    {
      "tags": ["Static", "SV", "Alignments viewer"],
      "name": "GenomeView",
      "img": "genomeview.png",
      "url": "https://github.com/nspies/genomeview",
      "pub": {
        "doi": "https://doi.org/10.1101/355636",
        "year": 2018,
        "citations": 2
      },
      "language": ["Python"],
      "width": 900,
      "height": 591,
      "github_stars": 140
    },
    {
      "name": "GenomeView (java app)",
      "img": "genomeview_java.png",
      "url": "https://genomeview.org/content/quick-start-guide",
      "github": "https://github.com/GenomeView/genomeview",
      "pub": {
        "doi": "https://doi.org/10.1093/nar/gkr995",
        "year": 2011,
        "citations": 118
      },
      "language": ["Java"],
      "tags": ["Alignments viewer"],
      "width": 640,
      "height": 496,
      "github_stars": 7
    },
    {
      "tags": ["Static", "Comparative"],
      "name": "genoPlotR",
      "img": "genoplotr.png",
      "url": "http://genoplotr.r-forge.r-project.org/",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btq413",
        "year": 2010,
        "citations": 569
      },
      "language": ["R"],
      "width": 500,
      "height": 300
    },
    {
      "tags": ["Static", "Ideogram", "Circular"],
      "name": "ggbio",
      "url": "http://www.bioconductor.org/packages/2.11/bioc/vignettes/ggbio/inst/doc/ggbio.pdf",
      "github": "https://github.com/lawremi/ggbio",
      "img": "ggbio.png",
      "language": ["R", "ggplot2"],
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      "tags": ["Comparative"],
      "name": "gggenomes",
      "url": "https://github.com/thackl/gggenomes",
      "img": "gggenomes.png",
      "pub": {
        "doi": "http://dx.doi.org/10.1101/2020.11.30.404863",
        "year": 2020,
        "citations": 3
      },
      "language": ["R"],
      "platform": ["Package"],
      "width": 3000,
      "height": 1200,
      "github_stars": 561
    },
    {
      "tags": ["Comparative", "Linear", "Quantitative"],
      "name": "GIVE",
      "github": "https://github.com/Zhong-Lab-UCSD/Genomic-Interactive-Visualization-Engine",
      "img": "give_hic.png",
      "url": "https://zhong-lab-ucsd.github.io/GIVE_homepage/",
      "language": ["JS"],
      "pub": {
        "doi": "https://doi.org/10.1186/s13059-018-1465-6",
        "year": 2018,
        "citations": 16
      },
      "platform": ["Web"],
      "width": 1680,
      "height": 1050,
      "github_stars": 142
    },
    {
      "tags": ["Comparative"],
      "name": "mauve-viewer",
      "img": "mauve_viewer.png",
      "url": "https://github.com/nconrad/mauve-viewer",
      "language": ["JS"],
      "platform": ["Web"],
      "width": 2112,
      "height": 1367,
      "github_stars": 40
    },
    {
      "tags": ["Comparative", "Dotplot", "Linear"],
      "name": "MCScan (python version)",
      "img": "mcscan_python.png",
      "url": "https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)",
      "github": "https://github.com/tanghaibao/jcvi",
      "language": ["Python"],
      "pub": {
        "doi": "10.1186/s13059-014-0573-1",
        "year": 2015,
        "citations": 327
      },
      "platform": ["CLI"],
      "width": 833,
      "height": 257,
      "github_stars": 702
    },
    {
      "name": "MCScanX",
      "tags": ["Comparative", "Dotplot", "Circular", "Linear", "Ideogram"],
      "url": "https://github.com/wyp1125/MCScanX",
      "img": "mcscanx.png",
      "pub": {
        "doi": "https://dx.doi.org/10.1093%2Fnar%2Fgkr1293",
        "year": 2012,
        "citations": 4123
      },
      "language": ["Perl"],
      "platform": ["CLI"],
      "width": 1424,
      "height": 1380,
      "github_stars": 198
    },
    {
      "tags": ["Comparative", "Deadlink"],
      "name": "mGSV (multiple genome synteny viewer)",
      "img": "mgsv.jpg",
      "url": "https://github.com/kashmatic/mGSV",
      "pub": {
        "doi": "https://dx.doi.org/10.1186%2F1471-2105-13-190",
        "year": 2012,
        "citations": 17
      },
      "platform": ["Web", "Silo"],
      "width": 600,
      "height": 322,
      "github_stars": 5
    },
    {
      "tags": ["Comparative"],
      "name": "MizBee",
      "img": "mizbee.jpg",
      "language": ["Processing"],
      "url": "http://www.cs.utah.edu/~miriah/mizbee/Overview.html",
      "platform": ["Desktop"],
      "pub": {
        "url": "https://ieeexplore.ieee.org/document/5290692",
        "doi": "10.1109/TVCG.2009.167",
        "year": 2009,
        "citations": 119
      },
      "width": 550,
      "height": 355
    },
    {
      "tags": ["Comparative"],
      "name": "Multiple genome viewer",
      "img": "mgv.png",
      "url": "http://www.informatics.jax.org/mgv/",
      "github": "https://github.com/mgijax/mgv",
      "language": ["JS", "VueJS"],
      "platform": ["Web", "Silo"],
      "pub": {
        "doi": "https://doi.org/10.1007/s00335-021-09904-1",
        "year": 2021,
        "citations": 4
      },
      "width": 512,
      "height": 341,
      "github_stars": 11
    },
    {
      "tags": ["Comparative", "Gene order"],
      "name": "OMA local synteny browser",
      "img": "oma.png",
      "pub": {
        "doi": "http://doi.org/10.1093/nar/gkaa1007",
        "year": 2020,
        "citations": 145
      },
      "url": "https://omabrowser.org/oma/synteny/ADH1A_HUMAN/",
      "platform": ["Web", "Silo"],
      "width": 1848,
      "height": 688
    },
    {
      "tags": ["Comparative", "Dotplot", "Linear"],
      "name": "pafr",
      "img": "pafr.png",
      "url": "https://github.com/dwinter/pafr",
      "language": ["R", "ggplot2"],
      "width": 672,
      "height": 960,
      "github_stars": 61
    },
    {
      "tags": ["Comparative"],
      "name": "Parasight",
      "img": "parasight.png",
      "url": "https://baileylab.brown.edu/parasight/galframe.html",
      "note": "Examples at https://ratparalogy.gs.washington.edu/",
      "pub": {
        "doi": "https://doi.org/10.1038/ng1562",
        "year": 2005,
        "citations": 741
      },
      "language": ["Perl"],
      "width": 570,
      "height": 285
    },
    {
      "tags": ["Comparative"],
      "name": "progressiveMauve viewer",
      "img": "progressive_mauve.png",
      "github": "https://github.com/koadman/mauve",
      "language": ["Java"],
      "url": "http://darlinglab.org/mauve/user-guide/viewer.html",
      "platform": ["Desktop"],
      "width": 638,
      "height": 512,
      "github_stars": 22
    },
    {
      "tags": ["Comparative", "Dotplot", "Linear"],
      "name": "SyMap",
      "url": "http://www.agcol.arizona.edu/software/symap/",
      "platform": ["Desktop"],
      "img": "symap.png",
      "pub": {
        "doi": "https://dx.doi.org/10.1101%2Fgr.5396706",
        "year": 2006,
        "citations": 155
      },
      "width": 640,
      "height": 1131
    },
    {
      "tags": ["Comparative"],
      "name": "Synima",
      "img": "synima.png",
      "url": "https://github.com/rhysf/Synima",
      "platform": ["CLI"],
      "language": ["Perl"],
      "pub": {
        "doi": "https://dx.doi.org/10.1186%2Fs12859-017-1939-7",
        "year": 2017,
        "citations": 37
      },
      "width": 778,
      "height": 539,
      "github_stars": 59
    },
    {
      "tags": ["Comparative"],
      "img": "jax_synteny_browser.png",
      "name": "Synteny browser",
      "url": "https://github.com/TheJacksonLaboratory/syntenybrowser",
      "platform": ["Web"],
      "width": 1848,
      "height": 815,
      "github_stars": 4
    },
    {
      "tags": ["Comparative", "Dotplot", "Linear", "Microbiology"],
      "name": "SynTView",
      "img": "syntview.png",
      "url": "http://hub18.hosting.pasteur.fr/SynTView/documentation/",
      "platform": ["Desktop", "Web", "Flash"],
      "pub": {
        "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849071/",
        "doi": "https://dx.doi.org/10.1186%2F1471-2105-14-277",
        "year": 2013,
        "citations": 22
      },
      "width": 1361,
      "height": 1152
    },
    {
      "tags": ["Comparative", "Linear", "Dotplot"],
      "name": "SynVisio",
      "img": "synvisio.png",
      "language": ["JS", "D3"],
      "url": "https://synvisio.github.io/",
      "github": "https://github.com/kiranbandi/synvisio",
      "width": 1920,
      "height": 1080,
      "github_stars": 74
    },
    {
      "tags": ["Comparative", "Ideogram"],
      "name": "Tripal MapViewer",
      "language": ["PHP", "JS"],
      "github": "https://github.com/statonlab/tripal_map",
      "img": "tripal_mapviewer.png",
      "pub": {
        "doi": "https://doi.org/10.1093/database/baz100",
        "year": 2019,
        "citations": 4
      },
      "width": 1000,
      "height": 435,
      "github_stars": 1
    },
    {
      "tags": ["Comparative"],
      "name": "VISTA browser",
      "url": "http://pipeline.lbl.gov/cgi-bin/gateway2",
      "img": "vista.png",
      "platform": ["Web", "Silo"],
      "pub": {
        "doi": "https://dx.doi.org/10.1093%2Fnar%2Fgkh458",
        "year": 2004,
        "citations": 1813
      },
      "width": 1222,
      "height": 348
    },
    {
      "tags": ["Comparative"],
      "name": "XMatchView",
      "img": "xmatchview.png",
      "github": "https://github.com/bcgsc/xmatchview",
      "language": ["Python"],
      "url": "https://www.bcgsc.ca/resources/software/xmatchview",
      "platform": ["Desktop"],
      "pub": {
        "doi": "https://doi.org/10.21105/joss.00497",
        "year": 2018,
        "citations": 3
      },
      "width": 1000,
      "height": 500,
      "github_stars": 36
    },
    {
      "tags": ["Graph"],
      "name": "AGB assembly graph browser",
      "img": "agb.jpeg",
      "github": "https://github.com/almiheenko/AGB",
      "platform": ["Web"],
      "language": ["Python"],
      "pub": {
        "url": "https://academic.oup.com/bioinformatics/article/35/18/3476/5306331",
        "doi": "https://doi.org/10.1093/bioinformatics/btz072",
        "year": 2019,
        "citations": 13
      },
      "github_stars": 77,
      "width": 1975,
      "height": 1044
    },
    {
      "tags": ["Graph"],
      "name": "Bandage",
      "img": "bandage.png",
      "url": "https://github.com/rrwick/Bandage/",
      "note": "See also BandageNG https://github.com/asl/BandageNG",
      "language": ["C++"],
      "platform": ["Desktop"],
      "pub": {
        "url": "https://academic.oup.com/bioinformatics/article/31/20/3350/196114",
        "doi": "https://doi.org/10.1093/bioinformatics/btv383",
        "year": 2015,
        "citations": 1636
      },
      "width": 440,
      "height": 157,
      "github_stars": 565
    },
    {
      "tags": ["Graph"],
      "name": "gfaestus",
      "img": "gfaestus.png",
      "url": "https://github.com/chfi/gfaestus",
      "note": "See demo video displaying GFF3 annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4",
      "language": ["Rust"],
      "width": 679,
      "height": 448,
      "github_stars": 61
    },
    {
      "tags": ["SV", "CNV", "Breakends", "Graph"],
      "name": "gGnomes",
      "img": "ggnomesr.png",
      "url": "https://github.com/mskilab/gGnome",
      "language": ["R"],
      "platform": ["Web"],
      "width": 1536,
      "height": 1920,
      "github_stars": 37
    },
    {
      "tags": ["SV", "CNV", "Breakends", "Graph"],
      "name": "gGnomes.js",
      "img": "ggnomes.png",
      "url": "https://github.com/mskilab/gGnome.js",
      "language": ["JS"],
      "platform": ["Web"],
      "width": 1222,
      "height": 575,
      "github_stars": 26
    },
    {
      "tags": ["Graph"],
      "name": "graphgenomeviewer",
      "img": "graphgenomeviewer.png",
      "url": "https://cmdcolin.github.io/graphgenomeviewer/",
      "github": "https://github.com/cmdcolin/graphgenomeviewer/",
      "language": ["JS"],
      "platform": ["Web"],
      "width": 1222,
      "height": 575,
      "github_stars": 8
    },
    {
      "tags": ["Graph", "Alignments viewer", "Circular", "SV"],
      "name": "MoMi-G",
      "img": "momig.png",
      "url": "https://github.com/MoMI-G/MoMI-G",
      "pub": {
        "doi": "10.1186/s12859-019-3145-2",
        "year": 2019,
        "citations": 21
      },
      "language": ["JS"],
      "platform": ["Web"],
      "width": 2880,
      "height": 1754,
      "github_stars": 85
    },
    {
      "tags": ["Graph"],
      "name": "odgi draw + odgi viz + odgi inject",
      "language": ["C++"],
      "github": "https://github.com/pangenome/odgi",
      "img": "odgi.png",
      "pub": {
        "doi": "https://doi.org/10.1101/2021.11.10.467921",
        "year": 2021,
        "citations": 14
      },
      "note": "Example from https://github.com/pangenome/pggb, see also gene arrow map https://odgi.readthedocs.io/en/latest/rst/tutorials/injecting_gene_arrows.html",
      "url": "https://odgi.readthedocs.io/en/latest/index.html",
      "width": 1389,
      "height": 1587,
      "github_stars": 180
    },
    {
      "tags": ["Graph"],
      "name": "sequence tube map",
      "img": "sequence_tube_map.png",
      "url": "https://github.com/vgteam/sequenceTubeMap",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btz597",
        "year": 2019,
        "citations": 29
      },
      "language": ["JS"],
      "platform": ["Web"],
      "width": 1594,
      "height": 422,
      "github_stars": 170
    },
    {
      "tags": ["Text based", "MSA"],
      "name": "Alan",
      "img": "alan.png",
      "url": "https://github.com/mpdunne/alan",
      "language": ["Bash"],
      "platform": ["CLI"],
      "width": 1096,
      "height": 712,
      "github_stars": 111
    },
    {
      "tags": ["Text based", "MSA"],
      "name": "Alv",
      "img": "alv.png",
      "url": "https://github.com/arvestad/alv",
      "pub": {
        "doi": "https://doi.org/10.21105/joss.00955",
        "year": 2018,
        "citations": 3
      },
      "platform": ["CLI"],
      "language": ["Python"],
      "width": 2244,
      "height": 598,
      "github_stars": 106
    },
    {
      "tags": ["Text based", "Alignments viewer"],
      "name": "ASCIIGenome",
      "img": "asciigenome.png",
      "url": "https://github.com/dariober/ASCIIGenome",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btx007",
        "year": 2017,
        "citations": 4
      },
      "language": ["Java"],
      "platform": ["CLI"],
      "width": 1368,
      "height": 632,
      "github_stars": 194
    },
    {
      "tags": ["Text based", "Coverage"],
      "name": "Bamcov",
      "img": "bamcov.png",
      "url": "https://github.com/fbreitwieser/bamcov",
      "language": ["C"],
      "platform": ["CLI"],
      "width": 637,
      "height": 166,
      "github_stars": 96
    },
    {
      "tags": ["Text based"],
      "name": "BLAST+ (reading -outfmt 0 pairwise output is the original CLI bioinformatics!)",
      "url": "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/",
      "pub": {
        "doi": "10.1186/1471-2105-10-421",
        "year": 2009,
        "citations": 13680
      },
      "language": ["C++"],
      "platform": ["CLI"]
    },
    {
      "tags": ["Text based"],
      "name": "Hapviz",
      "url": "https://github.com/ekg/hapviz",
      "img": "hapviz.png",
      "language": ["C"],
      "platform": ["CLI"],
      "width": 870,
      "height": 416,
      "github_stars": 11
    },
    {
      "tags": ["Text based"],
      "name": "plotReads",
      "img": "plotreads.png",
      "url": "http://campuspress.yale.edu/knightlab/ruddle/plotreads/",
      "platform": ["CLI", "Static"],
      "width": 2842,
      "height": 1634
    },
    {
      "name": "pyBamView",
      "tags": ["Alignments viewer", "Static"],
      "url": "https://mgymrek.github.io/pybamview/",
      "platform": ["CLI"],
      "img": "pybamview.png",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btu565",
        "year": 2014,
        "citations": 6
      },
      "note": "See supplementary info for more figures, supports padded SAM/BAM which is fairly rare",
      "language": ["Python"],
      "width": 644,
      "height": 695
    },
    {
      "tags": ["Text based"],
      "name": "Rna Alignment Viewers (Colorstock, SScolor, Ratón)",
      "url": "http://biowiki.org/wiki/index.php?title=Rna_Alignment_Viewers&redirect=no",
      "img": "rnaalignment.png",
      "platform": ["CLI"],
      "language": ["Perl"],
      "pub": {
        "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109877/",
        "doi": "https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtm635",
        "year": 2008,
        "citations": 3
      },
      "width": 544,
      "height": 286
    },
    {
      "tags": ["Text based"],
      "name": "Sam2pairwise",
      "url": "https://github.com/mlafave/sam2pairwise",
      "pub": {
        "doi": "https://doi.org/10.5281/zenodo.11377"
      },
      "language": ["C++"],
      "platform": ["CLI"],
      "github_stars": 40
    },
    {
      "tags": ["Text based", "Coverage"],
      "name": "Samtools depth visualization",
      "language": ["C"],
      "img": "depthplot.png",
      "url": "https://twitter.com/yokofakun/status/1178686978541441025",
      "platform": ["CLI", "GNUplot"],
      "width": 1101,
      "height": 446
    },
    {
      "tags": ["Text based", "Alignments viewer"],
      "name": "Samtools tview",
      "url": "http://www.htslib.org/",
      "github": "https://github.com/samtools/samtools",
      "language": ["C"],
      "platform": ["CLI"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btp352",
        "year": 2009,
        "citations": 45890
      },
      "img": "tview.png",
      "width": 1290,
      "height": 875,
      "github_stars": 1571
    },
    {
      "tags": ["Text based"],
      "name": "SvABA",
      "img": "svaba.png",
      "url": "https://github.com/walaj/svaba#alignmentstxtgz",
      "pub": {
        "doi": "https://doi.org/10.1101/gr.221028.117",
        "year": 2018,
        "citations": 279
      },
      "platform": ["CLI"],
      "width": 5360,
      "height": 1587,
      "github_stars": 225
    },
    {
      "tags": ["Text based"],
      "name": "VizAln (from HipSTR)",
      "img": "hipstr.png",
      "url": "https://github.com/tfwillems/HipSTR",
      "pub": {
        "doi": "https://doi.org/10.1038/nmeth.4267",
        "year": 2017,
        "citations": 214
      },
      "width": 4750,
      "height": 2046,
      "github_stars": 92
    },
    {
      "tags": ["Circular"],
      "name": "Anvio",
      "github": "https://github.com/merenlab/anvio",
      "pub": {
        "doi": "https://doi.org/10.7717/peerj.1319",
        "year": 2015,
        "citations": 1369
      },
      "url": "https://peerj.com/articles/1319/",
      "language": ["Python"],
      "github_stars": 406
    },
    {
      "tags": ["Circular"],
      "name": "BioCircos.js",
      "img": "biocircos.png",
      "language": ["JS"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btw041",
        "year": 2016,
        "citations": 114
      },
      "url": "http://bioinfo.ibp.ac.cn/biocircos/",
      "platform": ["Web"],
      "width": 900,
      "height": 600
    },
    {
      "tags": ["Commercial", "Circular"],
      "name": "Circa",
      "img": "circa.png",
      "url": "https://omgenomics.com/circa",
      "platform": ["Desktop"],
      "width": 1158,
      "height": 1158
    },
    {
      "tags": ["Circular", "Static"],
      "name": "Circleator",
      "github": "https://github.com/jonathancrabtree/Circleator",
      "img": "circleator.png",
      "url": "http://jonathancrabtree.github.io/Circleator/index.html",
      "pub": {
        "doi": "https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtu505",
        "year": 2014,
        "citations": 32
      },
      "language": ["Perl"],
      "width": 420,
      "height": 420,
      "github_stars": 46
    },
    {
      "tags": ["Circular", "Static"],
      "name": "circlize",
      "img": "circlize.jpeg",
      "url": "https://github.com/jokergoo/circlize",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btu393",
        "year": 2014,
        "citations": 2665
      },
      "language": ["R"],
      "width": 1181,
      "height": 1181,
      "github_stars": 948
    },
    {
      "tags": ["Circular", "Static"],
      "name": "Circos",
      "img": "circos.png",
      "note": "no official github to my knowledge",
      "url": "http://circos.ca/",
      "pub": {
        "doi": "https://dx.doi.org/10.1101%2Fgr.092759.109",
        "year": 2009,
        "citations": 8128
      },
      "language": ["Perl"],
      "width": 310,
      "height": 427,
      "github_stars": 68
    },
    {
      "tags": ["Circular"],
      "name": "CircosJS",
      "language": ["JS"],
      "img": "circosjs.png",
      "url": "https://github.com/nicgirault/circosJS",
      "platform": ["Web"],
      "width": 888,
      "height": 905,
      "github_stars": 503
    },
    {
      "tags": ["Circular"],
      "name": "DNAPlotter",
      "img": "dnaplotter.jpg",
      "url": "https://www.sanger.ac.uk/science/tools/dnaplotter",
      "pub": {
        "doi": "http://dx.doi.org/10.1093%2Fbioinformatics%2Fbtn578",
        "year": 2008,
        "citations": 693
      },
      "platform": ["Desktop"],
      "language": ["Java"],
      "width": 663,
      "height": 577
    },
    {
      "tags": ["Circular", "Linear"],
      "name": "GenomeProjector",
      "url": "https://github.com/gaou/g-language/wiki",
      "github": "https://github.com/gaou/g-language",
      "img": "glanguage.jpg",
      "platform": ["Desktop"],
      "language": ["Perl"],
      "pub": {
        "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2636772/",
        "doi": "https://dx.doi.org/10.1186%2F1471-2105-10-31",
        "year": 2009,
        "citations": 32
      },
      "width": 1024,
      "height": 768,
      "github_stars": 1
    },
    {
      "tags": ["Circular", "Static", "Comparative"],
      "name": "JupiterPlot",
      "img": "jupiterplot.png",
      "url": "https://github.com/JustinChu/JupiterPlot",
      "pub": {
        "doi": "https://doi.org/10.5281/zenodo.1241235"
      },
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      "height": 324,
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    },
    {
      "tags": ["Static"],
      "name": "mummer2circos",
      "img": "mummer2circos.png",
      "url": "https://github.com/metagenlab/mummer2circos",
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      "width": 3000,
      "height": 3000,
      "github_stars": 92
    },
    {
      "tags": ["Circular", "Static"],
      "name": "OGDRAW",
      "img": "ogdraw.png",
      "url": "https://chlorobox.mpimp-golm.mpg.de/OGDraw.html",
      "platform": ["Web"],
      "pub": {
        "doi": "https://doi.org/10.1093/nar/gkz238",
        "year": 2019,
        "citations": 1164
      },
      "width": 1250,
      "height": 1250
    },
    {
      "tags": ["Synthetic biology"],
      "img": "seqviz.png",
      "name": "seqviz",
      "url": "https://github.com/Lattice-Automation/seqviz#viewer",
      "platform": ["Web"],
      "width": 1848,
      "height": 633,
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    },
    {
      "tags": ["Synthetic biology"],
      "img": "aplasmideditor.png",
      "twitter": "https://twitter.com/apeplasmid?lang=en",
      "name": "ApE (a plasmid editor)",
      "url": "https://jorgensen.biology.utah.edu/wayned/ape/",
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      "width": 828,
      "height": 1725
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      "tags": [
        "Historical",
        "Deadlink",
        "Gene structure",
        "Annotation",
        "Comparative"
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      "name": "Apollo",
      "img": "apollo.jpg",
      "url": "https://web.archive.org/web/20060927154956/http://www.fruitfly.org/annot/apollo/",
      "note": "URL is an archive.org link",
      "platform": ["Desktop"],
      "language": ["Java"],
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        "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151184/",
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      "width": 600,
      "height": 247
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    {
      "tags": ["Gene structure", "Annotation", "JBrowse integration"],
      "img": "webapollo.jpg",
      "name": "Apollo aka WebApollo",
      "github": "https://github.com/gmod/apollo",
      "url": "https://genomearchitect.readthedocs.io/en/latest/",
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      "pub": {
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        "citations": 306
      },
      "language": ["Java", "Groovy", "JS"],
      "width": 685,
      "height": 384,
      "github_stars": 123
    },
    {
      "tags": ["Synthetic biology"],
      "name": "Chopchop",
      "img": "chopchop.png",
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        "citations": 1139
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      "width": 1378,
      "height": 575
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    {
      "tags": ["Alignments viewer"],
      "name": "Chromatic",
      "url": "https://chromatic.nci.nih.gov/",
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      "language": ["WASM"],
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        "citations": 4
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      "width": 1019,
      "height": 673
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    {
      "tags": ["CNV", "Annotation", "Deadlink"],
      "name": "cnvCurator",
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      "img": "cnvcurator.png",
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      "height": 476
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    {
      "tags": ["Gene structure", "Coverage", "Variation"],
      "interactive": ["true"],
      "name": "D3GB",
      "github": "https://github.com/BioinfoUSAL/D3GB",
      "note": "Live link http://d3gb.usal.es/docs/HumanGenomeBrowser/index.html?r=12:121113963-121213963 doesn't work anymore",
      "img": "d3gb.png",
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        "citations": 13
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      "platform": ["Web"],
      "width": 970,
      "height": 360,
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    {
      "tags": ["Exotic"],
      "img": "dnaskittle.png",
      "github": "https://github.com/josiahseaman/skittle",
      "language": ["Python", "JS"],
      "name": "DNASkittle",
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        "doi": "10.1186/1471-2105-10-452",
        "year": 2009,
        "citations": 7
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      "platform": ["Web"],
      "width": 1194,
      "height": 441,
      "github_stars": 7
    },
    {
      "tags": ["Epigenomics"],
      "name": "EaSeq",
      "img": "easeq.png",
      "url": "https://easeq.net/screenshots/",
      "platform": ["Desktop"],
      "pub": {
        "url": "https://www.nature.com/articles/nsmb.3180",
        "doi": "https://doi.org/10.1038/nsmb.3180",
        "year": 2016,
        "citations": 220
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      "width": 243,
      "height": 312
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    {
      "tags": ["Exotic"],
      "name": "FluentDNA",
      "img": "fluentdna.jpeg",
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      "pub": {
        "doi": "https://dx.doi.org/10.3389%2Ffgene.2020.00292",
        "year": 2020,
        "citations": 3
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      "platform": ["Web"],
      "width": 256,
      "height": 256
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    {
      "tags": ["Alignments viewer", "Linear"],
      "name": "Gambit",
      "img": "gambit.png",
      "url": "http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473",
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      "width": 1024,
      "height": 671
    },
    {
      "tags": ["SV", "Alignments viewer"],
      "name": "Ribbon",
      "language": ["JS"],
      "url": "http://genomeribbon.com/",
      "github": "https://github.com/MariaNattestad/ribbon",
      "img": "genomeribbon.png",
      "platform": ["Web"],
      "interactive": ["true"],
      "pub": {
        "url": "https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa680/5885081?redirectedFrom=fulltext",
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        "year": 2020,
        "citations": 47
      },
      "width": 720,
      "height": 405,
      "github_stars": 251
    },
    {
      "tags": ["CNV", "GWAS", "Linear", "MSA"],
      "name": "GenomeSpy",
      "img": "genomespy.png",
      "github": "https://github.com/genome-spy/genome-spy",
      "url": "https://genomespy.app/",
      "language": ["JS", "WebGL"],
      "platform": ["Web"],
      "interactive": ["true"],
      "width": 1194,
      "height": 476,
      "github_stars": 165
    },
    {
      "tags": ["General", "Linear"],
      "name": "Genoverse",
      "url": "https://github.com/wtsi-web/Genoverse",
      "language": ["JS"],
      "img": "genoverse.png",
      "platform": ["Web"],
      "width": 1194,
      "height": 476,
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    },
    {
      "tags": ["Linear", "Population"],
      "name": "Gnomad browser",
      "url": "https://github.com/macarthur-lab/gnomadjs",
      "language": ["JS"],
      "pub": {
        "doi": "https://doi.org/10.1038/s41586-020-2308-7",
        "year": 2020,
        "citations": 6107
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      "img": "gnomad.png",
      "twitter": "https://twitter.com/gnomad_project",
      "platform": ["Web", "Silo"],
      "width": 1081,
      "height": 599,
      "github_stars": 79
    },
    {
      "tags": ["SV", "Linear"],
      "name": "Gremlin",
      "img": "gremlin.png",
      "url": "http://compbio.cs.brown.edu/projects/gremlin/",
      "pub": {
        "doi": "https://doi.org/10.1109/tvcg.2010.163",
        "year": 2010,
        "citations": 22
      },
      "platform": ["Web"],
      "width": 1072,
      "height": 745
    },
    {
      "tags": ["Expression", "Linear", "Linkage disequilibrium"],
      "img": "gtex_locus.png",
      "name": "GTEX Locus browser",
      "pub": {
        "doi": "https://doi.org/10.1126/science.aaz1776",
        "year": 2020,
        "citations": 2497
      },
      "url": "https://gtexportal.org/home/locusBrowserPage/ACTN3",
      "platform": ["Web"],
      "width": 1194,
      "height": 767
    },
    {
      "tags": ["Population", "Linkage disequilibrium", "GWAS"],
      "name": "GWAS catalog browser",
      "img": "gwascatalog.png",
      "pub": {
        "doi": "https://doi.org/10.1093/nar/gky1120",
        "year": 2018,
        "citations": 3164
      },
      "url": "https://www.ebi.ac.uk/gwas/variants/rs1558902",
      "platform": ["Web"],
      "twitter": "https://twitter.com/gwascatalog?lang=en",
      "width": 748,
      "height": 533
    },
    {
      "tags": ["Alignments viewer", "Assembly QC"],
      "name": "Hawkeye",
      "github": "https://github.com/peterhj/amos",
      "language": ["C++"],
      "img": "hawkeye.png",
      "pub": {
        "url": "https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34",
        "doi": "10.1186/gb-2007-8-3-r34",
        "year": 2007,
        "citations": 55
      },
      "platform": ["Desktop"],
      "width": 1200,
      "height": 765,
      "github_stars": 0
    },
    {
      "tags": ["Population", "GWAS"],
      "name": "Human genome dating",
      "url": "https://human.genome.dating/region/chr1_13250000",
      "language": ["JS"],
      "platform": ["Web"],
      "img": "human_genome_dating.png",
      "pub": {
        "doi": "https://doi.org/10.1371/journal.pbio.3000586",
        "year": 2020,
        "citations": 136
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      "note": "made with vega/d3",
      "width": 1746,
      "height": 1352
    },
    {
      "tags": ["Assembly QC", "Graph"],
      "name": "Icarus QUAST",
      "img": "icarus.png",
      "url": "http://quast.sourceforge.net/icarus.html",
      "github": "https://github.com/ablab/quast",
      "platform": ["Web"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btw379",
        "year": 2016,
        "citations": 106
      },
      "width": 1504,
      "height": 797,
      "github_stars": 369
    },
    {
      "tags": ["SV", "Alignments viewer"],
      "name": "InGAP-SV",
      "img": "ingap_sv.png",
      "language": ["Java"],
      "url": "http://ingap.sourceforge.net/",
      "pub": {
        "doi": "10.1093/nar/gkr506",
        "year": 2011,
        "citations": 64
      },
      "platform": ["Desktop"],
      "width": 417,
      "height": 510
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    {
      "tags": ["SV", "Introgression"],
      "name": "Introgression browser",
      "img": "introgression_browser.png",
      "url": "https://git.wageningenur.nl/aflit001/ibrowser",
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        "url": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12800",
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        "year": 2015,
        "citations": 17
      },
      "language": ["Python"],
      "platform": ["Web"],
      "width": 619,
      "height": 359
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    {
      "tags": ["Microbiology", "Circular", "Linear"],
      "name": "IslandViewer and IslandPlot",
      "url": "https://bl.ocks.org/lairdm/c6c235dbfa6e6ee61565",
      "img": "islandplot.png",
      "language": ["JS", "D3"],
      "platform": ["Web"],
      "github": "https://github.com/lairdm/islandplot",
      "pub": {
        "doi": "https://doi.org/10.1093/nar/gkv401",
        "year": 2015,
        "citations": 251
      },
      "note": "web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG",
      "width": 937,
      "height": 374,
      "github_stars": 33
    },
    {
      "tags": ["Alignment viewer"],
      "name": "MagicViewer",
      "language": ["Java"],
      "img": "magicviewer.jpeg",
      "url": "http://bioinformatics.zj.cn/magicviewer/",
      "platform": ["Desktop"],
      "pub": {
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        "year": 2010,
        "citations": 40
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      "width": 1280,
      "height": 960
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    {
      "tags": ["GWAS", "Population"],
      "name": "Locuszoom",
      "github": "https://github.com/statgen/locuszoom",
      "img": "locuszoom.png",
      "url": "http://locuszoom.org/",
      "language": ["R", "Python"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btq419",
        "year": 2010,
        "citations": 2193
      },
      "platform": ["Web"],
      "width": 488,
      "height": 310,
      "github_stars": 149
    },
    {
      "name": "Locuszoom.js",
      "url": "http://locuszoom.org/locuszoomjs.php",
      "github": "https://github.com/statgen/locuszoom",
      "platform": ["Web"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btab186",
        "year": 2021,
        "citations": 155
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      "github_stars": 149
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    {
      "tags": ["Alignments viewer"],
      "name": "LookSeq",
      "github": "https://github.com/magnusmanske/lookseq",
      "img": "lookseq.png",
      "url": "https://www.sanger.ac.uk/tool/lookseq/",
      "pub": {
        "doi": "10.1101/gr.093443.109",
        "year": 2009,
        "citations": 50
      },
      "platform": ["Web"],
      "width": 1918,
      "height": 1049,
      "github_stars": 4
    },
    {
      "tags": ["Population"],
      "name": "Panoptes",
      "img": "panoptes.png",
      "github": "https://github.com/cggh/panoptes",
      "language": ["Python", "JS"],
      "url": "https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btx410",
        "year": 2017,
        "citations": 6
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      "width": 1378,
      "height": 476,
      "github_stars": 36
    },
    {
      "tags": ["Alignments viewer"],
      "name": "MapView",
      "img": "mapview.jpg",
      "url": "https://sites.google.com/site/wjwdavy/",
      "platform": ["Desktop"],
      "note": "links in original paper are dead, but URL provided here works",
      "pub": {
        "url": "https://academic.oup.com/bioinformatics/article/25/12/1554/193807",
        "doi": "https://doi.org/10.1093/bioinformatics/btp255",
        "year": 2009,
        "citations": 66
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      "width": 500,
      "height": 397
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    {
      "tags": ["Alignments viewer"],
      "name": "NGB",
      "img": "ngb.png",
      "url": "https://github.com/epam/NGB",
      "platform": ["Web"],
      "language": ["Java"],
      "width": 1920,
      "height": 921,
      "github_stars": 154
    },
    {
      "tags": ["Coverage"],
      "name": "SeqCover",
      "img": "seqcover.png",
      "github": "https://github.com/brentp/seqcover",
      "platform": ["Web"],
      "url": "https://brentp.github.io/seqcover/#gene=AIFM1",
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      "height": 476,
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    {
      "tags": ["Special-purpose"],
      "name": "SEQing",
      "img": "seqing.png",
      "url": "https://github.com/malewins/SEQing",
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        "doi": "https://doi.org/10.1186/s12859-020-3434-9",
        "year": 2020,
        "citations": 8
      },
      "language": ["Python"],
      "platform": ["Web"],
      "width": 1169,
      "height": 950,
      "github_stars": 8
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    {
      "tags": ["CNV"],
      "name": "SFARI",
      "url": "https://gene.sfari.org/database/human-gene/",
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        "doi": "https://doi.org/10.1242/dmm.005439",
        "year": 2010,
        "citations": 230
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      "img": "sfari.jpg",
      "platform": ["Web", "Silo"],
      "width": 745,
      "height": 367
    },
    {
      "tags": ["Alignments viewer"],
      "name": "Short read assembly browser",
      "img": "short_read_assembly_browser.png",
      "platform": ["Web", "Silo"],
      "pub": {
        "doi": "https://doi.org/10.1093/pcp/pcs183",
        "year": 2013,
        "citations": 575
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      "url": "https://rapdb.dna.affrc.go.jp/AssemblyBrowser2/index.html?ref=%22chr01%22&run_id=%22G4toI1%22&start=%22234780%22&end=%22236631%22",
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      "height": 476
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    {
      "tags": ["CNV"],
      "name": "SNPitty",
      "url": "https://bitbucket.org/ccbc/snpitty/src/master/",
      "language": ["R"],
      "img": "snpitty.jpg",
      "platform": ["Web"],
      "pub": {
        "url": "https://www.jmdjournal.org/article/S1525-1578(17)30166-6/fulltext",
        "doi": "https://doi.org/10.1016/j.jmoldx.2017.11.011",
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        "citations": 14
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    {
      "tags": ["MSA", "Deadlink"],
      "name": "SNIPViz",
      "github": "https://github.com/yeastrc/snipviz",
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      "url": "http://www.yeastrc.org/snipviz/4.HTML_Config_retrieve_newick_and_fasta_from_server/snip_viz_HTML_config_with_newick_clustering.html",
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      "platform": ["Web"],
      "width": 1377,
      "height": 519,
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    {
      "tags": ["SV", "CNV"],
      "name": "SplitThreader",
      "img": "splitthreader.png",
      "github": "https://github.com/MariaNattestad/SplitThreader",
      "language": ["JS", "PHP"],
      "url": "http://splitthreader.com/",
      "pub": {
        "doi": "https://doi.org/10.1101/087981",
        "year": 2016,
        "citations": 11
      },
      "platform": ["Web"],
      "width": 2698,
      "height": 1778,
      "github_stars": 66
    },
    {
      "tags": ["Alignments viewer", "Assembly QC"],
      "name": "Staden",
      "language": ["C", "Tcl/Tk"],
      "img": "staden.png",
      "url": "https://sourceforge.net/projects/staden/",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btq268",
        "year": 2010,
        "citations": 187
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      "platform": ["Desktop"],
      "width": 640,
      "height": 939
    },
    {
      "tags": ["Pangenome"],
      "name": "TASUKE",
      "img": "tasuke.png",
      "url": "https://ricegenome.dna.affrc.go.jp/",
      "note": "info about multi-genome-browser https://tasuke.dna.affrc.go.jp/",
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        "doi": "https://doi.org/10.1093/dnares/dsz022",
        "year": 2019,
        "citations": 21
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      "platform": ["Web"],
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      "height": 572
    },
    {
      "tags": ["Transposons", "Repeats", "Deadlink"],
      "language": ["Perl"],
      "platform": ["Web", "CGI", "Server"],
      "name": "TE-nest",
      "img": "tenest.jpg",
      "github": "https://github.com/cmdcolin/TEnest",
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        "year": 2007,
        "citations": 55
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      "note": "this was an online tool that does not appear to exist anymore see https://web.archive.org/web/20170712104431/http://www.plantgdb.org/tool/TEnest/. the github link is re-hosted source code also downloaded from archive.org",
      "width": 637,
      "height": 847,
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    {
      "tags": ["Transposons", "Repeats"],
      "name": "Transposcope",
      "github": "https://github.com/FenyoLab/transposcope",
      "img": "transposcope.png",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btaa244",
        "year": 2020,
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      },
      "language": ["JS"],
      "platform": ["Web"],
      "width": 1374,
      "height": 510,
      "github_stars": 8
    },
    {
      "tags": ["Special-purpose"],
      "name": "UGENE",
      "language": ["C++"],
      "img": "ugene.png",
      "url": "http://ugene.net/",
      "github": "https://github.com/ugeneunipro/ugene",
      "platform": ["Desktop"],
      "pub": {
        "doi": "10.1093/bioinformatics/bts091",
        "year": 2012,
        "citations": 2033
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      "width": 796,
      "height": 602,
      "github_stars": 201
    },
    {
      "tags": ["Annotation"],
      "name": "Varsome",
      "img": "varsome.png",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/bty897",
        "year": 2018,
        "citations": 1128
      },
      "url": "https://varsome.com/security-validation/?next=/variant/hg19/NM_000088.3(COL1A1):c.658C%3ET",
      "platform": ["Web", "Silo"],
      "width": 1378,
      "height": 572
    },
    {
      "tags": ["Splicing"],
      "name": "Vials",
      "pub": {
        "doi": "10.1109/TVCG.2015.2467911",
        "year": 2016,
        "citations": 16
      },
      "url": "http://vials.io/",
      "github": "https://github.com/Caleydo/vials",
      "platform": ["Web"],
      "github_stars": 13
    },
    {
      "tags": ["Quantitative"],
      "name": "wasm bigwig demo browser",
      "img": "wasm_bigwig.png",
      "url": "https://shk656461.github.io/index.html",
      "language": ["WASM"],
      "platform": ["Web"],
      "width": 977,
      "height": 279
    },
    {
      "tags": ["General"],
      "name": "BasePlayer",
      "url": "https://baseplayer.fi/",
      "github": "https://github.com/rkataine/BasePlayer",
      "img": "baseplayer.png",
      "platform": ["Desktop"],
      "language": ["Java"],
      "pub": {
        "url": "https://www.biorxiv.org/content/10.1101/126482v1.full",
        "doi": "https://doi.org/10.1038/s41596-018-0052-3",
        "year": 2018,
        "citations": 27
      },
      "width": 858,
      "height": 486,
      "github_stars": 4
    },
    {
      "tags": ["General", "Historical", "Alignments viewer"],
      "img": "celera.jpeg",
      "name": "Celera genome browser",
      "url": "https://www.csee.umbc.edu/~turner/presentations/bvw2002/sld009.htm",
      "platform": ["Desktop"],
      "width": 800,
      "height": 600
    },
    {
      "tags": ["General", "Alignments viewer"],
      "name": "IGB",
      "img": "igb.jpg",
      "url": "https://bioviz.org/",
      "platform": ["Desktop"],
      "language": ["Java"],
      "pub": {
        "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937187/",
        "doi": "https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtw069",
        "year": 2016,
        "citations": 309
      },
      "width": 800,
      "height": 398
    },
    {
      "tags": ["General", "Alignments viewer", "SV", "Quantitative"],
      "name": "IGV",
      "img": "igv.jpg",
      "language": ["Java"],
      "url": "https://igv.org/",
      "github": "https://github.com/igvteam/igv",
      "platform": ["Desktop"],
      "pub": {
        "doi": "https://dx.doi.org/10.1038%2Fnbt.1754",
        "year": 2011,
        "citations": 11116
      },
      "width": 1124,
      "height": 1280,
      "github_stars": 615
    },
    {
      "tags": ["General", "SV", "Alignments 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 viewer"],
      "name": "Tablet",
      "github": "https://github.com/cropgeeks/tablet",
      "img": "tablet.jpeg",
      "language": ["Java"],
      "url": "https://ics.hutton.ac.uk/tablet/",
      "pub": {
        "doi": "https://doi.org/10.1093/bib/bbs012",
        "year": 2012,
        "citations": 764
      },
      "platform": ["Desktop"],
      "width": 520,
      "height": 408,
      "github_stars": 37
    },
    {
      "tags": ["Exotic", "GWAS"],
      "name": "BigTop",
      "language": ["JS"],
      "img": "bigtop.png",
      "url": "https://blog.dnanexus.com/2019-05-21-bigtop-data-visualization/",
      "github": "https://github.com/dnanexus/bigtop",
      "platform": ["Web"],
      "width": 537,
      "height": 310,
      "github_stars": 5
    },
    {
      "tags": ["Exotic"],
      "name": "Cylindrical alignment app",
      "img": "cylindrical_alignment_viewer.png",
      "url": "https://sourceforge.net/projects/cylindrical-alignment-app/",
      "alt_url": "https://sourceforge.net/projects/cyl-viewer/",
      "platform": ["Desktop"],
      "width": 1920,
      "height": 1080
    },
    {
      "tags": ["General", "Alignments 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": 1143
      },
      "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": 22
      },
      "width": 1549,
      "height": 777,
      "github_stars": 156
    },
    {
      "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": 980
      },
      "url": "https://higlass.io",
      "platform": ["Web", "Server"],
      "width": 1250,
      "height": 956,
      "github_stars": 304
    },
    {
      "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": 624
    },
    {
      "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": 626
      },
      "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": 190
    },
    {
      "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": 102
      },
      "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": 5610
      },
      "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": 223
      },
      "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": 142
      },
      "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": 432
      },
      "url": "http://dgenies.toulouse.inra.fr/",
      "img": "dgenies.png",
      "language": ["JS", "Python", "D3"],
      "platform": ["Web"],
      "width": 500,
      "height": 500,
      "github_stars": 93
    },
    {
      "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": 1713
      },
      "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": 58
      },
      "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": 577
      },
      "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": 4337
      },
      "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"],
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      "pub": {
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        "doi": "https://doi.org/10.1186/s12859-021-04056-0",
        "year": 2021,
        "citations": 12
      },
      "tags": ["Assembly QC"],
      "img": "alvis_chimeric.png",
      "width": 708,
      "height": 396,
      "github_stars": 18
    },
    {
      "name": "genevisR",
      "img": "genevisr.png",
      "github": "https://github.com/griffithlab/GenVisR",
      "url": "https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btw325",
        "year": 2016,
        "citations": 237
      },
      "tags": ["CNV"],
      "language": ["R"],
      "width": 939,
      "height": 1026,
      "github_stars": 203
    },
    {
      "name": "NanoMethViz",
      "github": "https://github.com/Shians/NanoMethViz",
      "pub": {
        "doi": "10.1371/journal.pcbi.1009524",
        "year": 2021,
        "citations": 9
      },
      "url": "http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html",
      "img": "nanomethviz.png",
      "tags": ["Methylation"],
      "language": ["R"],
      "width": 672,
      "height": 480,
      "github_stars": 21
    },
    {
      "name": "GfaViz",
      "img": "gfaviz.png",
      "github": "https://github.com/ggonnella/gfaviz",
      "language": ["C++"],
      "pub": {
        "url": "https://academic.oup.com/bioinformatics/article/35/16/2853/5267826",
        "doi": "https://doi.org/10.1093/bioinformatics/bty1046",
        "year": 2018,
        "citations": 20
      },
      "tags": ["Graph"],
      "width": 951,
      "height": 351,
      "github_stars": 63
    },
    {
      "name": "Nextclade",
      "img": "nextclade.png",
      "url": "https://clades.nextstrain.org/",
      "language": ["JS", "React", "D3"],
      "tags": ["Phylogenetics", "Microbiology"],
      "pub": {
        "doi": "https://doi.org/10.21105/joss.03773",
        "year": 2021,
        "citations": 541
      },
      "note": "Related usage on nextstrain app also",
      "width": 1378,
      "height": 431
    },
    {
      "name": "vcfR",
      "img": "vcfr.png",
      "language": ["R"],
      "tags": ["Population", "Coverage"],
      "note": "image shows chromoqc output",
      "url": "https://knausb.github.io/vcfR_documentation/",
      "github": "https://github.com/knausb/vcfR",
      "pub": {
        "doi": "http://dx.doi.org/10.1111/1755-0998.12549",
        "year": 2016,
        "citations": 621
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      "width": 1344,
      "height": 1344,
      "github_stars": 237
    },
    {
      "name": "asgart",
      "img": "asgart.png",
      "language": ["Rust"],
      "github": "https://github.com/delehef/asgart",
      "tags": ["SV", "Ideogram", "Circular", "Linear"],
      "pub": {
        "url": "https://academic.oup.com/bioinformatics/article/34/16/2708/4948616",
        "doi": "https://doi.org/10.1093/bioinformatics/bty172",
        "year": 2018,
        "citations": 12
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      "width": 500,
      "height": 581,
      "github_stars": 31
    },
    {
      "name": "MashMap",
      "img": "mashmap.png",
      "tags": ["Dotplot"],
      "language": ["Perl", "C++"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/bty597",
        "year": 2018,
        "citations": 113
      },
      "url": "https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot",
      "github": "https://github.com/marbl/MashMap",
      "width": 521,
      "height": 521,
      "github_stars": 259
    },
    {
      "name": "udon",
      "img": "udon.png",
      "tags": ["Alignments viewer"],
      "url": "https://github.com/ocxtal/udon",
      "language": ["Rust"],
      "note": "Uses an advanced data structure for pileup, so visually a basic example but likely just a small demo",
      "width": 652,
      "height": 140,
      "github_stars": 20
    },
    {
      "name": "AnnoJ",
      "img": "annoj.png",
      "tags": ["Methylation"],
      "language": ["JS"],
      "platform": ["Web"],
      "url": "https://brainome.ucsd.edu/howto_annoj.html",
      "note": "See list of instances of the browser here https://ecker.salk.edu/genome-browser/",
      "github": "https://github.com/mukamel-lab/annoj_cndd",
      "width": 859,
      "height": 722,
      "github_stars": 0
    },
    {
      "name": "methylartist",
      "img": "methylartist.png",
      "language": ["Python"],
      "tags": ["Long reads", "Methylation"],
      "pub": {
        "doi": "https://doi.org/10.1101/2021.07.22.453313",
        "year": 2021,
        "citations": 7
      },
      "url": "https://github.com/adamewing/methylartist",
      "width": 1330,
      "height": 683,
      "github_stars": 114
    },
    {
      "name": "SWAV",
      "tags": ["Population", "Deadlink"],
      "pub": {
        "url": "https://www.nature.com/articles/s41598-019-57038-x",
        "doi": "https://doi.org/10.1038/s41598-019-57038-x",
        "year": 2020,
        "citations": 12
      },
      "url": "http://swav.popgenetics.net/",
      "img": "swav.png",
      "width": 1900,
      "height": 1386
    },
    {
      "name": "gingko",
      "url": "http://qb.cshl.edu/ginkgo/?q=/9EiUttUP0CBHs3WnuBa0",
      "img": "gingko.jpeg",
      "language": ["PHP", "JS"],
      "github": "https://github.com/robertaboukhalil/ginkgo",
      "pub": {
        "doi": "https://doi.org/10.1038/nmeth.3578",
        "year": 2015,
        "citations": 215
      },
      "platform": ["Web"],
      "tags": ["Single cell", "CNV"],
      "width": 2000,
      "height": 1400,
      "github_stars": 46
    },
    {
      "name": "copynumber",
      "url": "https://www.bioconductor.org/packages/release/bioc/vignettes/copynumber/inst/doc/copynumber.pdf",
      "img": "copynumber.png",
      "pub": {
        "doi": "https://doi.org/10.1186/1471-2164-13-591",
        "year": 2012,
        "citations": 239
      },
      "tags": ["CNV"],
      "language": ["R"],
      "width": 925,
      "height": 621
    },
    {
      "name": "alignfigR",
      "img": "alignfigr.png",
      "url": "https://cran.r-project.org/web/packages/alignfigR/vignettes/my-vignette.html",
      "tags": ["MSA"],
      "language": ["R"],
      "width": 528,
      "height": 240
    },
    {
      "name": "copykat",
      "img": "copykat.png",
      "url": "https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf",
      "github": "https://github.com/navinlabcode/copykat",
      "pub": {
        "doi": "10.1038/s41587-020-00795-2",
        "year": 2021,
        "citations": 337
      },
      "tags": ["Single cell", "CNV"],
      "language": ["R"],
      "width": 812,
      "height": 752,
      "github_stars": 191
    },
    {
      "name": "scCNV_heatmap",
      "url": "https://github.com/StefanKurtenbach/scCNV_heatmap",
      "language": ["Python"],
      "img": "sccnv_heatmap.png",
      "tags": ["Single cell", "CNV"],
      "width": 228,
      "height": 304,
      "github_stars": 3
    },
    {
      "name": "casper",
      "url": "https://github.com/akdess/CaSpER",
      "pub": {
        "url": "https://www.nature.com/articles/s41467-019-13779-x",
        "doi": "https://doi.org/10.1038/s41467-019-13779-x",
        "year": 2020,
        "citations": 98
      },
      "language": ["R"],
      "img": "casper.png",
      "tags": ["Single cell", "CNV"],
      "width": 580,
      "height": 935,
      "github_stars": 76
    },
    {
      "name": "RectChr",
      "img": "rectchr.png",
      "url": "https://github.com/BGI-shenzhen/RectChr",
      "tags": ["Comparative", "Ideogram", "Static", "Limited code available"],
      "language": ["Binary blob", "Perl"],
      "width": 635,
      "height": 760,
      "github_stars": 73
    },
    {
      "name": "LDBlockShow",
      "url": "https://github.com/BGI-shenzhen/LDBlockShow",
      "pub": {
        "url": "https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbaa227/5939575?redirectedFrom=fulltext",
        "doi": "https://doi.org/10.1093/bib/bbaa227",
        "year": 2020,
        "citations": 192
      },
      "img": "ldblockshow.png",
      "language": ["C++", "Perl"],
      "tags": ["GWAS", "Population"],
      "width": 260,
      "height": 275,
      "github_stars": 129
    },
    {
      "name": "clinker (gene fusion software)",
      "url": "https://github.com/Oshlack/Clinker/",
      "pub": {
        "url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6065480/",
        "doi": "https://dx.doi.org/10.1093%2Fgigascience%2Fgiy079",
        "year": 2018,
        "citations": 18
      },
      "img": "clinker_fusion.png",
      "tags": ["Gene fusion"],
      "language": ["R"],
      "width": 644,
      "height": 717,
      "github_stars": 50
    },
    {
      "name": "arriba",
      "img": "arriba.png",
      "tags": ["Gene fusion"],
      "url": "https://github.com/suhrig/arriba",
      "pub": {
        "url": "https://genome.cshlp.org/content/31/3/448",
        "doi": "10.1101/gr.257246.119",
        "year": 2021,
        "citations": 226
      },
      "language": ["C++", "R"],
      "width": 480,
      "height": 280,
      "github_stars": 211
    },
    {
      "name": "FusionInspector",
      "img": "fusioninspector.png",
      "url": "https://github.com/FusionInspector/FusionInspector/wiki",
      "github": "https://github.com/FusionInspector/FusionInspector",
      "pub": {
        "doi": "https://doi.org/10.1101/2021.08.02.454639",
        "year": 2021,
        "citations": 3
      },
      "tags": ["Gene fusion"],
      "note": "Uses igv.js",
      "language": ["Perl", "JS"],
      "width": 1889,
      "height": 811,
      "github_stars": 53
    },
    {
      "name": "NeoLoopFinder",
      "img": "neoloopfinder.png",
      "url": "https://github.com/XiaoTaoWang/NeoLoopFinder",
      "tags": ["SV", "Hi-C"],
      "pub": {
        "doi": "https://doi.org/10.1038/s41592-021-01164-w",
        "year": 2021,
        "citations": 77
      },
      "language": ["Python"],
      "width": 992,
      "height": 609,
      "github_stars": 52
    },
    {
      "name": "alen",
      "url": "https://github.com/jakobnissen/alen",
      "tags": ["MSA", "Text based"],
      "language": ["Rust"],
      "img": "alen.png",
      "width": 823,
      "height": 486,
      "github_stars": 75
    },
    {
      "name": "Aquaria",
      "url": "http://aquaria.ws/Q9HD67/5i0i/A",
      "tags": ["Protein", "MSA"],
      "pub": {
        "doi": "https://doi.org/10.1038/nmeth.3258",
        "year": 2015,
        "citations": 55
      },
      "platform": ["Web"],
      "img": "aquaria.png",
      "width": 1244,
      "height": 701
    },
    {
      "name": "vega",
      "url": "http://vega.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=6-QBL",
      "tags": ["Assembly QC", "Historical", "Genetic map"],
      "platform": ["Web"],
      "pub": {
        "doi": "https://doi.org/10.1093/nar/gki135",
        "year": 2004,
        "citations": 91
      },
      "img": "vega.png",
      "note": "Mentioned in https://www.biorxiv.org/content/10.1101/2021.07.02.450883v1.full.pdf also note: vega standards for vertebrate genome annotation database",
      "width": 1523,
      "height": 798
    },
    {
      "name": "nightingale/protvista",
      "github": "https://github.com/ebi-webcomponents/nightingale",
      "url": "https://ebi-webcomponents.github.io/nightingale/#/msa",
      "tags": ["Protein", "MSA"],
      "platform": ["Web"],
      "pub": {
        "doi": "https://dx.doi.org/10.1093%2Fbioinformatics%2Fbtx120",
        "year": 2017,
        "citations": 56
      },
      "img": "nightingale.png",
      "language": ["JS", "Typescript"],
      "note": "Used on InterProScan website https://www.ebi.ac.uk/interpro/",
      "width": 1211,
      "height": 425,
      "github_stars": 116
    },
    {
      "name": "ArchR",
      "github": "https://github.com/GreenleafLab/ArchR",
      "url": "https://www.archrproject.com/articles/Articles/tutorial.html",
      "pub": {
        "doi": "https://doi.org/10.1038/s41588-021-00790-6",
        "year": 2021,
        "citations": 655
      },
      "tags": ["Single cell"],
      "language": ["R"],
      "img": "archr.png",
      "width": 1500,
      "height": 1500,
      "github_stars": 359
    },
    {
      "name": "PGAP-X",
      "img": "pgapx.png",
      "tags": ["Pangenome"],
      "language": ["C++"],
      "platform": ["Desktop"],
      "url": "https://pgapx.zhaopage.com/",
      "pub": {
        "url": "https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4337-7",
        "doi": "https://doi.org/10.1186/s12864-017-4337-7",
        "year": 2018,
        "citations": 23
      },
      "width": 778,
      "height": 248
    },
    {
      "name": "MAVIS",
      "img": "mavis.png",
      "github": "https://github.com/bcgsc/mavis",
      "tags": ["Gene fusion", "SV"],
      "language": ["Python"],
      "url": "http://mavis.bcgsc.ca/",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/bty621",
        "year": 2018,
        "citations": 22
      },
      "width": 1200,
      "height": 494,
      "github_stars": 72
    },
    {
      "name": "ProViz",
      "img": "proviz.png",
      "tags": ["MSA", "Protein"],
      "language": ["JS"],
      "url": "http://slim.icr.ac.uk/proviz/index.php",
      "note": "See also alphafold visualization as tracks 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": 48
    },
    {
      "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": 42
      },
      "width": 840,
      "height": 510,
      "github_stars": 276
    },
    {
      "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": 867
      },
      "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": 7184
      },
      "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": 11616
      },
      "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": {
        "url": "https://www.biorxiv.org/content/10.1101/2021.04.29.441969v1.full.pdf",
        "doi": "https://doi.org/10.1101/2021.04.29.441969",
        "year": 2021,
        "citations": 44
      },
      "tags": ["Comparative", "Dotplot", "Circular"],
      "width": 1247,
      "height": 392,
      "github_stars": 105
    },
    {
      "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": 164
      },
      "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": {
        "url": "https://www.biorxiv.org/content/10.1101/2021.10.20.465046v1.full.pdf",
        "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 structure", "Epigenomics"],
      "language": ["R"],
      "width": 850,
      "height": 500,
      "github_stars": 124
    },
    {
      "name": "gcMapExplorer",
      "img": "gcmapexplorer.png",
      "url": "https://github.com/rjdkmr/gcMapExplorer",
      "pub": {
        "doi": "https://doi.org/10.1093/nar/gkx644",
        "year": 2017,
        "citations": 24
      },
      "tags": ["Hi-C"],
      "language": ["Python"],
      "width": 576,
      "height": 309,
      "github_stars": 21
    },
    {
      "name": "BRIG",
      "img": "brig.jpg",
      "github": "https://github.com/happykhan/BRIG",
      "tags": ["Comparative", "Circular"],
      "url": "http://brig.sourceforge.net",
      "pub": {
        "url": "https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-402",
        "doi": "https://doi.org/10.1186/1471-2164-12-402",
        "year": 2011,
        "citations": 2364
      },
      "language": ["Java"],
      "platform": ["Desktop"],
      "width": 1200,
      "height": 1075,
      "github_stars": 25
    },
    {
      "name": "Ideogram 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": 82
      },
      "note": "Includes a powerful analysis pipeline, worth reading the paper",
      "language": ["R"],
      "width": 730,
      "height": 593,
      "github_stars": 174
    },
    {
      "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": 1570
      },
      "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": 2882
      },
      "width": 2100,
      "height": 1050,
      "github_stars": 809
    },
    {
      "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": 401
      },
      "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": 1058
      },
      "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": 2
      },
      "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": 85
      },
      "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": 1223
      },
      "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": 49
      },
      "width": 703,
      "height": 393,
      "github_stars": 90
    },
    {
      "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": 294
      },
      "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": 42
      },
      "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": 265
    },
    {
      "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": 738
      },
      "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 viewer"],
      "language": ["Java"],
      "pub": {
        "doi": "https://dx.doi.org/10.1186%2F1471-2105-13-S7-S12",
        "year": 2012,
        "citations": 2
      },
      "url": "http://genovar.sourceforge.net/",
      "width": 575,
      "height": 472
    },
    {
      "name": "VAMP",
      "img": "vamp.jpg",
      "language": ["Java"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btl359",
        "year": 2006,
        "citations": 89
      },
      "tags": ["Deadlink", "CNV", "ArrayCGH"],
      "platform": ["Applet", "Desktop"],
      "width": 520,
      "height": 399
    },
    {
      "name": "CGH-Explorer",
      "img": "cghexplorer.jpg",
      "language": ["Java"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/bti113",
        "year": 2004,
        "citations": 114
      },
      "tags": ["Deadlink", "CNV", "ArrayCGH"],
      "platform": ["Desktop"],
      "width": 520,
      "height": 324
    },
    {
      "name": "GenomeMatcher",
      "img": "genomematcher.png",
      "language": ["Objective-C"],
      "twitter": "https://twitter.com/GenomeMatcher",
      "url": "http://www.ige.tohoku.ac.jp/joho/gmProject/gmmanual.html",
      "tags": ["Comparative"],
      "platform": ["Desktop", "Mac"],
      "pub": {
        "doi": "https://doi.org/10.1186/1471-2105-9-376",
        "year": 2008,
        "citations": 225
      },
      "width": 600,
      "height": 679
    },
    {
      "name": "DNAVis",
      "img": "dnavis.png",
      "language": ["C++", "OpenGL"],
      "platform": ["Desktop"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/bti807",
        "year": 2005,
        "citations": 6
      },
      "tags": ["Deadlink", "Comparative"],
      "width": 679,
      "height": 803
    },
    {
      "name": "SynBrowse",
      "img": "synbrowse.png",
      "language": ["Perl"],
      "platform": ["Web"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/bti555",
        "year": 2005,
        "citations": 53
      },
      "tags": ["Comparative", "GBrowse integration"],
      "width": 520,
      "height": 446
    },
    {
      "name": "Sybil",
      "img": "sybil.png",
      "language": ["Perl"],
      "platform": ["Web"],
      "pub": {
        "doi": "https://doi.org/10.1007/978-1-59745-547-3_6",
        "year": 2007,
        "citations": 52
      },
      "tags": ["Comparative", "GBrowse integration"],
      "url": "http://sybil.sourceforge.net/",
      "note": "Download 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": 40
      },
      "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": 24
      },
      "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": 4609
      },
      "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": 163
      },
      "width": 1059,
      "height": 355,
      "github_stars": 267
    },
    {
      "name": "numbat",
      "img": "numbat.png",
      "language": ["R"],
      "tags": ["Single cell", "CNV"],
      "pub": {
        "doi": "https://doi.org/10.1101/2022.02.07.479314",
        "year": 2022,
        "citations": 9
      },
      "url": "https://kharchenkolab.github.io/numbat/",
      "github": "https://github.com/kharchenkolab/numbat",
      "width": 840,
      "height": 672,
      "github_stars": 156
    },
    {
      "name": "ggtranscript",
      "img": "ggtranscript.png",
      "language": ["R"],
      "tags": ["Gene structure"],
      "url": "https://github.com/dzhang32/ggtranscript",
      "pub": {
        "doi": "https://doi.org/10.1101/2022.03.28.486050",
        "year": 2022,
        "citations": 2
      },
      "width": 2100,
      "height": 900,
      "github_stars": 117
    },
    {
      "name": "CIAlign",
      "note": "Has useful utility functions to clean gaps and trim MSAs",
      "img": "cialign.png",
      "language": ["Python"],
      "tags": ["MSA"],
      "pub": {
        "doi": "https://doi.org/10.7717/peerj.12983",
        "year": 2022,
        "citations": 35
      },
      "github": "https://github.com/KatyBrown/CIAlign",
      "width": 480,
      "height": 286,
      "github_stars": 104
    },
    {
      "name": "CoolBox",
      "img": "coolbox.png",
      "pub": {
        "doi": "https://doi.org/10.1186/s12859-021-04408-w",
        "year": 2021,
        "citations": 18
      },
      "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": 219
    },
    {
      "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": 6
      },
      "tags": ["CNV", "Large display", "No binary or source available"],
      "width": 770,
      "height": 355
    },
    {
      "name": "SequenceSurveyor",
      "language": ["Adobe AIR"],
      "img": "sequencesurveyor.png",
      "url": "https://graphics.cs.wisc.edu/Vis/SequenceSurveyor/index.html",
      "pub": {
        "doi": "http://dx.doi.org/10.1109/TVCG.2011.232",
        "year": 2011,
        "citations": 36
      },
      "tags": ["Comparative"],
      "width": 2016,
      "height": 1027
    },
    {
      "name": "BactoGENIE",
      "img": "bactogenie.png",
      "pub": {
        "doi": "https://doi.org/10.1186/1471-2105-16-S11-S6",
        "year": 2015,
        "citations": 8
      },
      "tags": [
        "Comparative",
        "Microbiology",
        "Large display",
        "No binary or source available"
      ],
      "width": 600,
      "height": 199
    },
    {
      "name": "PSAT",
      "img": "psat.png",
      "pub": {
        "doi": "https://doi.org/10.1186/1471-2105-9-170",
        "year": 2008,
        "citations": 27
      },
      "tags": ["Comparative", "Deadlink", "No binary or source available"],
      "platform": ["Web", "Silo"],
      "url": "http://www.nwrce.org/psat",
      "width": 496,
      "height": 200
    },
    {
      "name": "TreeBrowser (MicrobesOnline)",
      "img": "treegenome.png",
      "tags": ["Comparative", "GBrowse integration"],
      "pub": {
        "doi": "https://doi.org/10.1093/nar/gkp919",
        "year": 2009,
        "citations": 382
      },
      "url": "http://www.microbesonline.org/cgi-bin/treeBrowse.cgi?locus=17761",
      "platform": ["Web", "Silo"],
      "language": ["Perl"],
      "width": 462,
      "height": 431
    },
    {
      "name": "UTGB (University of Tokyo Genome Browser)",
      "img": "utgb.png",
      "language": ["Java"],
      "platform": ["Web", "Servlet"],
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/btp350",
        "year": 2009,
        "citations": 11
      },
      "tags": ["General"],
      "github": "https://github.com/utgenome/utgb",
      "url": "http://utgenome.org/",
      "width": 359,
      "height": 236,
      "github_stars": 2
    },
    {
      "name": "Argo",
      "img": "argo.png",
      "language": ["Java", "Applet"],
      "tags": ["General", "Deadlink"],
      "url": "https://web.archive.org/web/20070924141423/http://www.broad.mit.edu/annotation/argo/",
      "notes": "See also the tool 'Combo', a comparative version",
      "width": 450,
      "height": 338
    },
    {
      "name": "Combo",
      "img": "combo.png",
      "note": "Based on the tool '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": 2676
      },
      "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": 404
      },
      "width": 525,
      "height": 675,
      "github_stars": 492
    },
    {
      "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": 171
      },
      "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": 270
      },
      "language": ["R"],
      "tags": ["Ideogram", "Comparative"],
      "width": 620,
      "height": 646,
      "github_stars": 149
    },
    {
      "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 viewer",
        "Comparative",
        "Annotation",
        "Variation",
        "Expression"
      ],
      "name": "ERGO",
      "img": "ergo.png",
      "url": "https://www.igenbio.com/ergo",
      "width": 2590,
      "height": 2018,
      "pub": {
        "url": "https://pubmed.ncbi.nlm.nih.gov/12519973/",
        "doi": "https://doi.org/10.1093/nar/gkg148",
        "year": 2003,
        "citations": 166
      }
    },
    {
      "name": "modbamtools",
      "img": "modbamtools.png",
      "url": "https://github.com/rrazaghi/modbamtools",
      "language": ["Python"],
      "tags": ["Methylation", "Epigenomics"],
      "pub": {
        "doi": "https://doi.org/10.1101/2022.07.07.499188",
        "year": 2022,
        "citations": 9
      },
      "width": 750,
      "height": 619,
      "github_stars": 44
    },
    {
      "name": "sequenza",
      "img": "sequenza.png",
      "url": "https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.html#plots-and-results",
      "note": "also see https://sequenzatools.bitbucket.io/#/home",
      "language": ["R"],
      "tags": ["CNV"],
      "pub": {
        "doi": "https://doi.org/10.1093/annonc/mdu479",
        "year": 2015,
        "citations": 586
      },
      "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": 314,
      "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": 74,
      "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": 947
      },
      "tags": ["Local ancestry"],
      "width": 1024,
      "height": 768
    },
    {
      "name": "MOSAIC",
      "img": "mosaic.png",
      "url": "https://maths.ucd.ie/~mst/MOSAIC/",
      "language": ["R"],
      "tags": ["Local ancestry"],
      "pub": {
        "doi": "https://doi.org/10.1534/genetics.119.302139",
        "year": 2019,
        "citations": 55
      },
      "width": 727,
      "height": 320
    },
    {
      "name": "Prosite/MyDomains",
      "img": "prosite.png",
      "url": "https://prosite.expasy.org/mydomains",
      "tags": ["Protein"],
      "platform": ["Web", "Silo"],
      "pub": {
        "doi": "https://doi.org/10.1093/nar/gkm977",
        "year": 2007,
        "citations": 342
      },
      "width": 561,
      "height": 40
    },
    {
      "name": "snpit",
      "img": "snpit.png",
      "url": "https://github.com/aineniamh/snipit",
      "tags": ["Variation", "Population"],
      "language": ["Python"],
      "width": 750,
      "height": 306,
      "github_stars": 112
    },
    {
      "name": "local-rearrangements",
      "img": "local-rearrangements.png",
      "url": "https://github.com/mcfrith/local-rearrangements",
      "tags": ["Dotplot", "SV"],
      "language": ["Python"],
      "note": "Can color dotplots with annotations for e.g. exons, transposons, low complexity regions. 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": 82
      },
      "img": "ggmsa.png",
      "language": ["R"],
      "width": 825,
      "height": 188,
      "github_stars": 190,
      "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": 41
    },
    {
      "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": 666
      },
      "width": 1400,
      "height": 1920,
      "github_stars": 293
    },
    {
      "name": "pyGenomeViz",
      "url": "https://github.com/moshi4/pyGenomeViz",
      "tags": ["Comparative"],
      "language": ["Python"],
      "img": "pygenomeviz.png",
      "width": 1291,
      "height": 693,
      "github_stars": 238,
      "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/10.48550/arXiv.2205.06349"
      },
      "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 painting"],
      "url": "https://github.com/jordanlab/tagore",
      "width": 600,
      "height": 258,
      "github_stars": 35
    },
    {
      "name": "pileuppy",
      "img": "pileuppy.png",
      "language": ["Python"],
      "tags": ["Text based"],
      "url": "https://gitlab.com/tprodanov/pileuppy",
      "width": 1213,
      "height": 805
    },
    {
      "name": "ggcoverage",
      "img": "ggcoverage.png",
      "language": ["R"],
      "tags": ["Coverage", "Ideogram", "CNV", "Splicing"],
      "pub": {
        "doi": "https://doi.org/10.1101/2022.09.01.503744",
        "year": 2022,
        "citations": 1
      },
      "url": "https://cran.r-project.org/web/packages/ggcoverage/vignettes/ggcoverage.html",
      "github": "https://github.com/showteeth/ggcoverage",
      "width": 1024,
      "height": 717,
      "github_stars": 204
    },
    {
      "name": "python-genome-browser aka pygbrowse",
      "url": "https://github.com/phageghost/python-genome-browser/blob/master/pygbrowse_demonstration.ipynb",
      "github": "https://github.com/phageghost/python-genome-browser/",
      "img": "pygbrowse.png",
      "tags": ["Epigenomics", "Hi-C", "Coverage", "Gene structure"],
      "language": ["Python"],
      "width": 994,
      "height": 503,
      "github_stars": 27
    },
    {
      "name": "wally",
      "language": ["C++"],
      "img": "wally.png",
      "tags": ["Alignments viewer", "Dotplot", "SV"],
      "url": "https://github.com/tobiasrausch/wally",
      "github_stars": 97,
      "width": 676,
      "height": 538
    },
    {
      "name": "alignoth",
      "language": ["Rust", "Vega"],
      "tags": ["Alignments viewer"],
      "github": "https://github.com/koesterlab/alignoth",
      "url": "http://htmlpreview.github.io/?https://github.com/koesterlab/alignoth/blob/main/examples/plot.html",
      "img": "alignoth.png",
      "width": 1776,
      "height": 440,
      "github_stars": 51
    },
    {
      "name": "ezcharts",
      "img": "ezcharts.png",
      "tags": ["Ideogram"],
      "language": ["Python"],
      "github": "https://github.com/epi2me-labs/ezcharts",
      "width": 1141,
      "height": 569,
      "github_stars": 16
    },
    {
      "name": "gw",
      "img": "gw.png",
      "tags": ["Alignments viewer", "Variation"],
      "language": ["C++", "OpenGL"],
      "github": "https://github.com/kcleal/gw",
      "width": 2492,
      "height": 618,
      "github_stars": 143
    },
    {
      "name": "PretextView",
      "img": "pretextview.jpg",
      "tags": ["Hi-C", "OpenGL"],
      "language": ["C++"],
      "github": "https://github.com/wtsi-hpag/PretextView",
      "width": 1616,
      "height": 1616,
      "github_stars": 26
    },
    {
      "name": "pyCirclize",
      "img": "pycirclize.png",
      "tags": ["Circular"],
      "language": ["Python"],
      "github": "https://github.com/moshi4/pyCirclize",
      "width": 1292,
      "height": 865,
      "github_stars": 645
    },
    {
      "name": "plasmapR",
      "img": "plasmapr.png",
      "tags": ["Synthetic biology", "Circular"],
      "language": ["R"],
      "github": "https://github.com/BradyAJohnston/plasmapR",
      "width": 2100,
      "height": 2100,
      "github_stars": 72
    },
    {
      "name": "DrukBam",
      "img": "drukbam.png",
      "github": "https://github.com/StephanHolgerD/DrukBam",
      "language": ["Python"],
      "tags": ["Alignments viewer"],
      "width": 1270,
      "height": 742,
      "github_stars": 19
    },
    {
      "github": "https://github.com/matted/genome_coverage_plotter",
      "name": "genome_coverage_plotter",
      "img": "genome-coverage-plotter.png",
      "language": ["Python"],
      "tags": ["CNV", "Coverage"],
      "github_stars": 6,
      "width": 1600,
      "height": 400
    },
    {
      "github": "https://github.com/mrvollger/NucFreq",
      "name": "NucFreq",
      "img": "nucfreq.png",
      "tags": ["Variation", "Coverage"],
      "language": ["Python", "R"],
      "width": 1600,
      "height": 400,
      "github_stars": 24
    },
    {
      "name": "PGR-TK",
      "github": "https://github.com/cschin/pgr-tk",
      "pub": {
        "doi": "10.1038/s41592-023-01914-y",
        "year": 2023,
        "citations": 9
      },
      "tags": ["Graph", "Pangenome"],
      "language": ["Rust"],
      "img": "pgrtk.png",
      "width": 1109,
      "height": 385,
      "github_stars": 11
    },
    {
      "name": "asynt",
      "github": "https://github.com/simonhmartin/asynt",
      "tags": ["Comparative", "Dotplot"],
      "img": "asynt.png",
      "language": ["R"],
      "width": 884,
      "height": 594,
      "github_stars": 24
    },
    {
      "name": "GeMo",
      "tags": ["Chromosome painting", "Ideogram"],
      "img": "gemo.png",
      "language": ["JS"],
      "github": "https://github.com/SouthGreenPlatform/GeMo",
      "pub": {
        "doi": "10.1093/database/baac057",
        "year": 2022,
        "citations": 2
      },
      "github_stars": 13,
      "width": 2250,
      "height": 2130
    },
    {
      "name": "NGenomeSyn",
      "tags": ["Comparative", "Multi-way synteny"],
      "img": "ngenomesyn.png",
      "language": ["Perl"],
      "pub": {
        "doi": "10.1093/bioinformatics/btad121",
        "year": 2023,
        "citations": 25
      },
      "github": "https://github.com/hewm2008/NGenomeSyn",
      "note": "See also RectChr",
      "width": 710,
      "height": 612,
      "github_stars": 137
    },
    {
      "name": "chromsyn",
      "img": "chromsyn.png",
      "github": "https://github.com/slimsuite/chromsyn",
      "tags": ["Comparative", "Multi-way synteny"],
      "language": ["R"],
      "doi": {
        "pub": "10.1101/2022.04.22.489119"
      },
      "width": 1500,
      "height": 975,
      "github_stars": 24
    },
    {
      "name": "pixy",
      "img": "pixy.png",
      "github": "https://github.com/ksamuk/pixy/",
      "url": "https://pixy.readthedocs.io/en/latest/plotting.html#a-genome-wide-plot-of-summary-statistics",
      "note": "The link in readthedocs shows a nice general purpose 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": 106,
      "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, 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 cell", "Strand-seq"],
      "img": "mosaicatcher.png",
      "github": "https://github.com/friendsofstrandseq/mosaicatcher-pipeline",
      "language": ["R", "Python", "SnakeMake"],
      "width": 2483,
      "height": 3524,
      "github_stars": 20
    },
    {
      "name": "TogoStanza Protein Browser",
      "img": "togostanza.png",
      "tags": ["Protein"],
      "language": ["JS"],
      "url": "https://db-dev.jpostdb.org/ts/stanza/protein_browser/help.html",
      "width": 1474,
      "height": 889
    },
    {
      "name": "ReConPlot",
      "img": "reconplot.png",
      "github": "https://github.com/cortes-ciriano-lab/ReConPlot",
      "language": ["R"],
      "tags": ["SV", "CNV"],
      "pub": {
        "doi": "10.1101/2023.02.24.529890",
        "year": 2023,
        "citations": 1
      },
      "width": 917,
      "height": 430,
      "github_stars": 18
    },
    {
      "name": "rich-msa",
      "language": ["Python"],
      "tags": ["Text based", "MSA"],
      "github": "https://github.com/althonos/rich-msa",
      "img": "richmsa.png",
      "width": 933,
      "height": 921,
      "github_stars": 77
    },
    {
      "name": "gtracks",
      "tags": ["General"],
      "language": ["Python"],
      "note": "Powered by 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": 5
    },
    {
      "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 structure", "Sashimi"],
      "language": ["Python"],
      "pub": {
        "doi": "https://doi.org/10.1371/journal.pcbi.1011477",
        "year": 2023,
        "citations": 1
      },
      "url": "https://github.com/ygidtu/trackplot",
      "width": 491,
      "height": 355,
      "github_stars": 64
    },
    {
      "name": "BAMdash",
      "url": "https://github.com/jonas-fuchs/BAMdash/",
      "img": "bamdash.png",
      "language": ["Python"],
      "tags": ["Coverage"],
      "width": 1494,
      "height": 636,
      "github_stars": 20
    },
    {
      "name": "ModDotPlot",
      "img": "moddotplot.png",
      "url": "https://github.com/marbl/ModDotPlot",
      "language": ["Python"],
      "pub": {
        "doi": "https://www.biorxiv.org/content/10.1101/2024.04.15.589623v1"
      },
      "tags": ["Comparative", "Dotplot", "Heatmap", "Repeats"],
      "width": 1926,
      "height": 1296,
      "github_stars": 92
    },
    {
      "name": "odp (oxford dot plots)",
      "img": "odp.png",
      "tags": ["Comparative", "Dotplot", "Snakemake", "Multi-way synteny"],
      "url": "https://github.com/conchoecia/odp",
      "language": ["Python"],
      "pub": {
        "doi": "https://doi.org/10.1038/s41586-023-05936-6",
        "year": 2023,
        "citations": 107
      },
      "note": "Pub is not for visualization tool, but it is suggested to cite this paper",
      "width": 1000,
      "height": 618,
      "github_stars": 113
    },
    {
      "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": 16
      },
      "tags": ["Circular", "Comparative", "Microbiology"],
      "width": 1500,
      "height": 1500,
      "github_stars": 66
    },
    {
      "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 toolkit)",
      "interactive": ["true"],
      "language": ["JS", "C++"],
      "tags": ["Graph"],
      "img": "sgtk.png",
      "url": "https://olga24912.github.io/SGTK/",
      "github": "https://github.com/olga24912/SGTK",
      "pub": {
        "doi": "https://doi.org/10.1093/bioinformatics/bty956",
        "year": 2018,
        "citations": 9
      },
      "width": 1371,
      "height": 337,
      "github_stars": 28
    },
    {
      "name": "pgv (graph tool)",
      "github": "https://github.com/w-gao/pgv",
      "url": "https://w-gao.github.io/pgv/",
      "img": "pgv2.png",
      "tags": ["Graph"],
      "language": ["JS", "Python"],
      "width": 1281,
      "height": 874,
      "github_stars": 18
    },
    {
      "name": "Panagram",
      "tags": ["K-mer", "Pangenome"],
      "url": "https://github.com/kjenike/panagram",
      "language": ["Python"],
      "img": "panagram.png",
      "width": 693,
      "height": 500,
      "github_stars": 53
    },
    {
      "name": "VAG",
      "pub": {
        "doi": "https://doi.org/10.1101/2023.01.20.524849",
        "year": 2023,
        "citations": 0
      },
      "tags": ["Graph", "Pangenome"],
      "img": "vag.jpg",
      "github": "https://github.com/lipingfangs/VAG",
      "language": ["Python", "JS"],
      "width": 1694,
      "height": 667,
      "github_stars": 17
    },
    {
      "name": "ntSynt",
      "img": "ntsynt.png",
      "language": ["R"],
      "tags": ["Comparative", "Multi-way synteny"],
      "github": "https://github.com/bcgsc/ntSynt/",
      "url": "https://github.com/bcgsc/ntSynt/tree/main/visualization_scripts",
      "pub": {
        "doi": "https://doi.org/10.1101/2024.02.07.579356",
        "year": 2024,
        "citations": 0
      },
      "note": "Uses 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": 17
    },
    {
      "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": 0
      },
      "width": 2882,
      "height": 1197,
      "github_stars": 160
    },
    {
      "name": "SVhawkeye",
      "img": "svhawkeye.jpg",
      "tags": ["SV", "Alignments viewer"],
      "language": ["Python", "R"],
      "url": "https://github.com/yywan0913/SVhawkeye",
      "pub": {
        "doi": "https://doi.org/10.3389/fgene.2024.1352443",
        "year": 2024,
        "citations": 0
      },
      "github_stars": 22,
      "width": 1065,
      "height": 576
    },
    {
      "name": "SeeNV",
      "img": "seenv.png",
      "url": "https://github.com/MSBradshaw/SeeNV",
      "pub": {
        "doi": "https://doi.org/10.1101/2024.05.08.593244",
        "year": 2024,
        "citations": 0
      },
      "language": ["Python"],
      "tags": ["CNV", "Population", "SV", "Coverage"],
      "width": 4868,
      "height": 5454,
      "github_stars": 2
    },
    {
      "name": "SYNY",
      "img": "syny.png",
      "url": "https://github.com/PombertLab/SYNY",
      "pub": {
        "doi": "https://doi.org/10.1101/2024.05.09.593317",
        "year": 2024,
        "citations": 0
      },
      "language": ["Perl", "Python"],
      "tags": [
        "Comparative",
        "Dotplot",
        "Circular",
        "Ideogram",
        "Multi-way synteny"
      ],
      "width": 1692,
      "height": 2446,
      "github_stars": 23
    },
    {
      "name": "chrov",
      "img": "chrov.png",
      "url": "https://github.com/rraadd88/chrov",
      "language": ["Python"],
      "tags": ["Ideogram", "Lollipops", "Circular", "CNV"],
      "note": "See also usage in https://github.com/rraadd88/beditor",
      "width": 576,
      "height": 1106,
      "github_stars": 3
    },
    {
      "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": 20
    },
    {
      "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
    }
  ]
}