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TOOLS.json
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{
"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": 53
},
"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": 9
},
{
"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": 29
},
{
"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": 2535
},
"platform": ["Desktop"],
"language": ["Java"],
"width": 400,
"height": 241,
"github_stars": 121
},
{
"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": 151
},
"width": 1956,
"height": 634,
"github_stars": 169
},
{
"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": 11
},
{
"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": 9
},
"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": 2419
},
"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": 8133
},
"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": 9
},
"platform": ["Web"],
"width": 413,
"height": 254,
"github_stars": 15
},
{
"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": 3
},
"platform": ["Web"],
"width": 1654,
"height": 290,
"github_stars": 31
},
{
"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": 312
},
"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": 24
},
{
"tags": ["MSA"],
"name": "pymsaplotter",
"language": ["Python"],
"img": "pymsaplotter.png",
"url": "https://github.com/orangeSi/pymsaploter",
"width": 1000,
"height": 513,
"github_stars": 14
},
{
"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": 19
},
{
"tags": ["MSA"],
"name": "seqotron",
"img": "seqotron.png",
"url": "https://github.com/4ment/seqotron",
"pub": {
"doi": "10.1186/s13104-016-1927-4",
"year": 2016,
"citations": 38
},
"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": 53
},
"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": 271
},
"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": 53
},
"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": 7
},
"width": 4000,
"height": 1800,
"github_stars": 28
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