346个基因组可视化工具一网打进！_flexidot

Github来源：https://github.com/cmdcolin/awesome-genome-visualization

配套网页：

https://cmdcolin.github.io/awesome-genome-visualization/?latest=true

工具名称、下载链接、文献、编程语言、运行平台如下

Ideogram viewer

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https://bioinformatics.mdanderson.org/public-software/ideogramviewer/

Language: JS

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Platform: Web

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BRIG

http://brig.sourceforge.net

Publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-402

Language: Java

Tags: Comparative, Circular

Platform: Desktop

GenomeMaps

http://www.genomemaps.org/

Publication: https://academic.oup.com/nar/article/41/W1/W41/1113984

Language: JS

Tags: General, Deadlink

gcMapExplorer

https://github.com/rjdkmr/gcMapExplorer

Language: Python

Tags: Hi-C

Trackplot

https://github.com/PoisonAlien/trackplot

Language: R

Tags: Coverage, Gene structure

REViewer

https://github.com/Illumina/REViewer

Publication: https://www.biorxiv.org/content/10.1101/2021.10.20.465046v1.full.pdf

Tags: Repeats

Note: See also GraphAlignmentViewer, similar look and from illumina also

PGV

https://github.com/ucrbioinfo/PGV

Publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04424-w

Language: Python

Tags: Pangenome, Dotplot, Comparative

Platform: Web

AmpliconArchitect

https://github.com/virajbdeshpande/AmpliconArchitect

Language: Python

Tags: SV, Cancer

Note: The term amplicon refers essentially to extrachromosomal DNA in cancer

WGDI

https://github.com/SunPengChuan/wgdi

Publication: https://www.biorxiv.org/content/10.1101/2021.04.29.441969v1.full.pdf

Language: Python

Tags: Comparative, Dotplot, Circular

AliTreeViz

https://www.npmjs.com/package/alitreeviz

Language: JS

Tags: MSA, Phylogenetics

Haploview

https://www.broadinstitute.org/haploview/haploview

Language: Java

Platform: Desktop

MEGA-X

https://www.megasoftware.net/

Tags: MSA, Phylogenetics

Platform: Desktop

GraphAlignmentViewer

https://github.com/Illumina/GraphAlignmentViewer

Tags: Repeats

PipMaker

http://pipmaker.bx.psu.edu/pipmaker/

Tags: Comparative, Repeat, Annotation

Note: See also MultiPipMaker http://pipmaker.bx.psu.edu/pipmaker/mpm-example/index.html

IGGE

https://github.com/immersivegraphgenomeexplorer/IGGE

Publication: https://www.researchgate.net/profile/Aviv-Elor/publication/354582953_The_Immersive_Graph_Genome_Explorer_Navigating_Genomics_in_Immersive_Virtual_Reality/links/6140c890578238365b0afa3a/The-Immersive-Graph-Genome-Explorer-Navigating-Genomics-in-Immersive-Virtual-Reality.pdf

Tags: Graph, Exotic

Note: Not open source

oxford-plots

https://github.com/jherrero/oxford-plots

Language: R, Perl

Tags: Dotplot

Note: Has nice description of a synteny pipeline here https://github.com/jherrero/oxford-plots/blob/master/examples/pig_X_Y.txt

MIRA

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Publication: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf

Language: C++

Tags: Assembly, Alignment viewer, Historical

Plotgardener

https://github.com/PhanstielLab/plotgardener/

Publication: https://www.biorxiv.org/content/10.1101/2021.09.08.459338v1

Language: R

Tags: Hi-C, Coverage

Flash Gviewer

http://gmod.org/wiki/Flashgviewer/

Language: Flash, ActionScript

Tags: Ideogram, Genetic Map, Historical

IdeoViz

https://www.bioconductor.org/packages/release/bioc/vignettes/IdeoViz/inst/doc/Vignette.pdf

Language: R

Tags: Ideogram, Quantitative, Splicing

genomegraphs

http://bioconductor.org/packages/2.5/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf

Language: R

Tags: Ideogram, Quantitative, Splicing

splicejam

https://github.com/jmw86069/splicejam

Language: R

Tags: Splicing, Sashimi

pretzel

https://github.com/plantinformatics/pretzel

Language: JS, D3

Tags: Comparative, Genetic map

wiggleplotr

http://bioconductor.org/packages/devel/bioc/vignettes/wiggleplotr/inst/doc/wiggleplotr.html

Language: R

Tags: Coverage

SVPV

https://github.com/VCCRI/SVPV

Publication: https://academic.oup.com/bioinformatics/article/33/13/2032/3056003

Language: Python

Tags: SV, Coverage

panGraphViewer

https://github.com/TF-Chan-Lab/panGraphViewer

Language: Python

Tags: Graph, Pangenome

ProViz

http://slim.icr.ac.uk/proviz/index.php

Publication: https://academic.oup.com/nar/article/44/W1/W11/2499309

Language: JS

Tags: MSA, Protein

Note: See also alphafold visualization as tracks http://slim.icr.ac.uk/projects/alphafold?page=alphafold_proviz_homepage

MAVIS

http://mavis.bcgsc.ca/

Language: Python

Tags: Gene fusion, SV

PGAP-X

https://pgapx.zhaopage.com/

Publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4337-7

Language: C++

Tags: Pangenome

Platform: Desktop

ArchR

https://www.archrproject.com/articles/Articles/tutorial.html

Language: R

Tags: Single cell

nightingale/protvista

https://ebi-webcomponents.github.io/nightingale/#/msa

Tags: Protein, MSA

Platform: Web

vega

http://vega.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=6-QBL

Tags: Assembly, Historical, Genetic map

Note: Mentioned in https://www.biorxiv.org/content/10.1101/2021.07.02.450883v1.full.pdf

Platform: Web

Aquaria

http://aquaria.ws/Q9HD67/5i0i/A

Tags: Protein, MSA

Platform: Web

alen

https://github.com/jakobnissen/alen

Language: Rust

Tags: MSA, Text based

NeoLoopFinder

https://github.com/XiaoTaoWang/NeoLoopFinder

Language: Python

Tags: SV, Hi-C

FusionInspector

https://github.com/FusionInspector/FusionInspector/wiki

Language: Perl, JS

Tags: Gene fusion

Note: Uses igv.js

arriba

https://github.com/suhrig/arriba

Publication: https://genome.cshlp.org/content/31/3/448

Language: C++, R

Tags: Gene fusion

clinker (gene fusion)

https://github.com/Oshlack/Clinker/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6065480/

Language: R

Tags: Gene fusion

LDBlockShow

https://github.com/BGI-shenzhen/LDBlockShow

Publication: https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbaa227/5939575?redirectedFrom=fulltext

Language: C++, Perl

Tags: GWAS, Population

RectChr

https://github.com/BGI-shenzhen/RectChr

Tags: Comparative, Ideogram, Static

casper

https://github.com/akdess/CaSpER

Publication: https://www.nature.com/articles/s41467-019-13779-x

Language: R

Tags: Single cell, CNV

scCNV_heatmap

https://github.com/StefanKurtenbach/scCNV_heatmap

Language: Python

Tags: Single cell, CNV

copykat

https://github.com/navinlabcode/copykat/blob/master/vignettes/copycat-vignettes.pdf

Language: R

Tags: Single cell, CNV

alignfigR

https://cran.r-project.org/web/packages/alignfigR/vignettes/my-vignette.html

Language: R

Tags: MSA

copynumber

https://www.bioconductor.org/packages/release/bioc/vignettes/copynumber/inst/doc/copynumber.pdf

Language: R

Tags: CNV

SWAV

http://swav.popgenetics.net/

Publication: https://www.nature.com/articles/s41598-019-57038-x

Tags: Population, Deadlink

methylartist

https://github.com/adamewing/methylartist

Language: Python

AnnoJ

https://brainome.ucsd.edu/howto_annoj.html

Language: JS

Tags: Methylation

Note: See list of instances of the browser here https://ecker.salk.edu/genome-browser/

Github: https://github.com/mukamel-lab/annoj_cndd

Platform: Web

udon

https://github.com/ocxtal/udon

Language: Rust

Tags: Alignment viewer

Note: Uses an advanced data structure for pileup, so visually a basic example but likely just a small demo

MashMap

https://github.com/marbl/MashMap/blob/master/scripts/generateDotPlot

Tags: Dotplot

asgart

https://github.com/delehef/asgart

Publication: https://academic.oup.com/bioinformatics/article/34/16/2708/4948616

Language: Rust

Tags: SV, Ideogram, Circular, Linear

vcfR

https://knausb.github.io/vcfR_documentation/

Language: R

Tags: QC, Population, Coverage

Note: image shows chromoqc output

Nextclade

https://clades.nextstrain.org/

Language: JS, React, D3

Tags: Phylogenetics

Note: Related usage on nextstrain app also

GfaViz

Publication: https://academic.oup.com/bioinformatics/article/35/16/2853/5267826

Language: C++

Tags: Graph

NanoMethViz

http://www.bioconductor.org/packages/release/bioc/html/NanoMethViz.html

Publication: https://www.biorxiv.org/content/10.1101/2021.01.18.426757v3

Language: R

Tags: Methylation

genevisR

https://bioconductor.org/packages/release/bioc/vignettes/GenVisR/inst/doc/Intro.html

Language: R

Tags: CNV

ALVIS (chimeric alignment viewer)

https://github.com/SR-Martin/alvis

Publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Tags: QC, Assembly

ALVIS (MSA viewer)

https://www.ebi.ac.uk/research/goldman/software/alvis

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856975/

Tags: MSA

Note: Introduces sequence bundles concept, also see web app version https://www.ebi.ac.uk/goldman-srv/sequencebundles/

mocha

https://github.com/freeseek/mocha#plot-results

Language: C, WDL, R

Tags: CNV

Note: Has a full analysis pipeline associated with end result visualizations

bctools cnv

https://samtools.github.io/bcftools/howtos/cnv-calling.html

Tags: CNV

bcftools roh

https://samtools.github.io/bcftools/howtos/roh-calling.html

Language: Python

Tags: Static

Note: Plots runs of homozygosity, has interactive plot-roh.py helper too

Internet Contig Explorer

https://www.bcgsc.ca/resources/software/ice

Publication: https://genome.cshlp.org/content/13/6a/1244.long

Tags: Historical

spinteny

https://github.com/skinner/spinteny

Tags: Exotic, Comparative

sockeye

https://www.bcgsc.ca/resources/software/sockeye

Publication: https://genome.cshlp.org/content/14/5/956.full

Tags: Exotic, Comparative

SMRT View

http://files.pacb.com/software/smrtanalysis/2.3.0/doc/smrtview/help/Webhelp/App_View_Epipro.htm

Tags: SV

Github: https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View

PURPLE

https://github.com/hartwigmedical/hmftools/blob/master/purity-ploidy-estimator/README.md

Tags: CNV, Cancer

Note: intermutation-distance rainfall plots/katagesis plots are not technically in genomic coordinates, but do indicate genomic cluster of variatnts

LINX

https://github.com/hartwigmedical/hmftools/blob/master/sv-linx/README_VIS.md

Tags: Graph, SV, Breakends, Circular, Linear, Gene fusion, Cancer

Note: part of the PURPLE/GRIDSS/LINX pipeline

Shasta

https://chanzuckerberg.github.io/shasta/ComputationalMethods.html#ReadGraph

Language: C++

Tags: Graph

Note: Uses graphviz

Platform: Web, Localhost, CLI

PopSV

https://github.com/jmonlong/PopSV/blob/master/3-Visualization.md

Language: R

Tags: Population, SV

Platform: Web

clinker

https://github.com/gamcil/clinker

Publication: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab007/6103786

Language: JS

Tags: Comparative, Gene order

Platform: Web

covviz

https://brwnj.github.io/covviz/

Language: JS

Tags: CNV, Coverage, Population

JGI/IMG

https://img.jgi.doe.gov/

Tags: Dotplot, Linear, Microbiology

Note: Dotplot use MUMmer

Platform: Web, Silo

FastANI

https://github.com/ParBLiSS/FastANI

Language: C++

Tags: Comparative, Microbiology

Gview

https://server.gview.ca/examples

Tags: Circular, Linear, Pangenome, Microbiology

Platform: Web

LinearDisplay.pl

https://github.com/JCVenterInstitute/LinearDisplay

Language: Perl

Tags: Comparative

Platform: CLI

REPAVER

https://gitlab.com/gringer/bioinfscripts/

Publication: https://www.researchgate.net/publication/346507956_REPAVER_Paving_the_Way_for_Repeat_Discovery_in_Complex_Genomes?channel=doi&linkId=5fc58ba4a6fdcce95268fe60&showFulltext=true

Language: R, C++

Tags: Repeats, Dotplot, Static, Linear

Platform: CLI

Dotter

https://sonnhammer.sbc.su.se/Dotter.html

Publication: https://pubmed.ncbi.nlm.nih.gov/8566757/

Tags: Dotplot

Platform: CLI

VIVA

https://www.biorxiv.org/content/10.1101/589879v1.full.pdf

Tags: Heatmap, Population, Variants

Platform: Web

UCSC Xena

https://xena.ucsc.edu/

Tags: Heatmap, Population

Platform: Web

pViz

https://github.com/Genentech/pviz

Tags: Protein

Platform: Web

GenomePaint

https://genomepaint.stjude.cloud/

Publication: https://www.cell.com/cancer-cell/fulltext/S1535-6108(20)30659-0

Tags: CNV, Linear, Cancer, Lollipops

Note: See also gallery here https://genomepaint.stjude.cloud/#figures

Platform: Web

ProteinPaint

https://pecan.stjude.cloud/proteinpaint

Publication: https://www.nature.com/articles/ng.3466

Tags: Protein, Cancer, Lollipops

Platform: Web

Protael

http://sanshu.github.io/protaelweb/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963358/

Language: JS

Tags: Protein, MSA

Platform: Web

RPAN (3kricedb)

http://cgm.sjtu.edu.cn/3kricedb/visualization/?tracks=DNA%2Cgene%2CPF

Tags: Pangenome, JBrowse integration

Platform: Web

Panache

https://github.com/SouthGreenPlatform/panache

Tags: Pangenome

Panacaea

https://github.com/JCVenterInstitute/PanACEA

Tags: Pangenome

Pan-Tetris

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547177/

Tags: Pangenome

iGenomics

https://www.biorxiv.org/content/10.1101/2020.02.11.944132v1

Tags: Mobile

UCSC Genome Graphs

http://genome.ucsc.edu/cgi-bin/hgGenome

Tags: Ideogram

Platform: Web, Form, Silo

NCBI Genome Decoration

https://www.ncbi.nlm.nih.gov/genome/tools/gdp/

Tags: Ideogram

Platform: Web, Form, Silo

KaryotypeSVG

https://github.com/andreasprlic/karyotypeSVG

Language: JS, SVG

Tags: Ideogram

Platform: Web

karyoploteR

https://github.com/bernatgel/karyoploteR

Language: R

Tags: Ideogram, Static

Ideogram

https://github.com/RCollins13/HumanIdiogramLibrary

Language: SVG

Tags: Ideogram, Static

eweitz/Ideogram

https://github.com/eweitz/ideogram

Language: JS

Tags: Ideogram

Platform: Web

chromoMap

https://www.biorxiv.org/content/10.1101/605600v1.full.pdf

Language: R

Tags: Ideogram, Static

Peax

https://github.com/Novartis/peax

Language: JS

Tags: Epigenomics, Higlass integration

Platform: Web

Juicebox.js

http://www.igv.org/doc/juiceboxjs.html

Publication: https://www.cell.com/fulltext/S2405-4712(18)30001-2

Language: JS

Tags: Epigenomics, Hi-C

Platform: Web

Juicebox

https://github.com/aidenlab/Juicebox

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596920/

Language: Java

Tags: Epigenomics, Hi-C

Platform: Desktop

HiPiler

http://hipiler.higlass.io

Tags: Epigenomics, Hi-C, Higlass integration

Platform: Web

Epiviz

https://epiviz.github.io/

Publication: https://www.biorxiv.org/content/10.1101/865295v1.full.pdf

Language: JS, R, D3

Tags: Epigenomics

Platform: Web

Epilogos

https://epilogos.altius.org/

Tags: Epigenomics, Higlass integration

Platform: Web

cisGenome Browser

https://jhui2014.github.io/browser/screenshots.html

Language: C

Tags: Epigenomics

Platform: Desktop

Chipster

https://chipster.csc.fi/

Language: Java

Tags: Epigenomics, CNV

Note: Copy number tutorial https://chipster.csc.fi/manual/cn-tutorial.pdf

Platform: Desktop

Chip Monk

http://www.bioinformatics.babraham.ac.uk/projects/chipmonk/

Language: Java

Tags: Epigenomics

Note: Also see SeqMonk https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/

Platform: Desktop

syntenyPlotByR

https://github.com/shingocat/syntenyPlotByR

Language: R

Tags: Dotplot, Static

Redottable

https://github.com/s-andrews/redotable

Language: Java

Tags: Dotplot

Platform: Desktop

ggplot2 mummerplot

https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/

Language: R

Tags: Dotplot

Mummerplot

http://mummer.sourceforge.net/

Language: GNUPlot

Tags: Dotplot, Static

Minidot

https://github.com/thackl/minidot

Language: R

Tags: Dotplot, Static

last-dotplot

http://last.cbrc.jp/

Tags: Dotplot

Platform: CLI, Web-server

Jdot

https://github.com/LyonsLab/jdot

Language: JS

Tags: Dotplot

Platform: Web

FlexiDot

https://github.com/molbio-dresden/flexidot

Language: Python

Tags: Dotplot

Platform: CLI

Dottup

https://www.bioinformatics.nl/cgi-bin/emboss/help/dottup

Tags: Dotplot

Note: also seen here http://eichlerlab.gs.washington.edu/publications/chm1-structural-variation/data/GRCh37/heterochromatic_extensions.pdf

dotPlotly

https://github.com/tpoorten/dotPlotly/

Language: R, Shiny

Tags: Dotplot

Platform: Web

Dotlet

https://dotlet.vital-it.ch/

Language: JS

Tags: Dotplot

Platform: Web

Dot

https://dot.sandbox.bio/

Tags: Dotplot

Github: https://github.com/MariaNattestad/dot

Platform: Web

Discoplot

https://github.com/mjsull/DiscoPlot

Language: Python

Tags: Dotplot, Static

Delly-maze

https://github.com/dellytools/maze

Language: Python

Tags: Dotplot, Static

D-GENIES

http://dgenies.toulouse.inra.fr/

Language: JS, Python, D3

Tags: Dotplot

Github: https://github.com/genotoul-bioinfo/dgenies

Platform: Web

cgplot

https://github.com/dfguan/cgplot

Language: Python

Tags: Static, Dotplot

Zenbu

http://fantom.gsc.riken.jp/zenbu/

Tags: General

Platform: Web

WashU epigenomics browser

https://epigenomegateway.wustl.edu/

Language: JS, React

Tags: General, Epigenomics, Hi-C

Platform: Web

Valis browser

https://valis.bio/

Language: JS, WebGL

Tags: General, Quantitative, Epigenomics

Platform: Web

UCSC genome browser

https://genome.ucsc.edu/

Tags: General

Platform: Web, Silo

Trackster

https://galaxyproject.org/learn/visualization/

Tags: General

Platform: Web

Pileup.js

https://github.com/hammerlab/pileup.js/

Language: JS

Tags: General, SV

Platform: Web

Nucleome browser

https://vis.nucleome.org/v1/main.html

Language: JS

Tags: General, Multi

Platform: Web

NCBI Genome Data Viewer

https://www.ncbi.nlm.nih.gov/genome/gdv/

Tags: General, SV, Epigenomics, Gene structure, Splicing

Platform: Web, Silo

Kero-BROWSE

https://kero.hgc.jp/examples/CLCL/hg38/index.html

Language: JS

Tags: General, SV, Alignment viewer

Platform: Web

JBrowse 2

http://jbrowse.org/jb2

Language: JS, Typescript, React

Tags: General, SV, Comparative, Dotplot, Circular, Alignment viewer, Quantitative, Hi-C

Note: See gallery for more examples https://jbrowse.org/jb2/gallery

Platform: Web

JBrowse

http://jbrowse.org/jbrowse1.html

Language: JS

Tags: General, Alignment viewer, SV, Quantitative, Gene structure

Note: See also JBrowse plugin registry https://gmod.github.io/jbrowse-registry. Runs on the web or as a desktop app using Electron

Platform: Web, Desktop

IGV.js

https://github.com/igvteam/igv.js/

Tags: General, Alignment viewer

Platform: Web

HiGlass

https://higlass.io

Language: JS, WebGL

Tags: General, Epigenomics, Hi-C

Platform: Web

Gosling

https://gosling.js.org/

Language: JS, WebGL, Typescript, React

Tags: General, Epigenomics, Higlass integration, Linear, Circular, Comparative, Quantitative

Platform: Web

GBrowse+GBrowse 2

http://gmod.org/wiki/GBrowse

Language: Perl

Tags: General

Platform: Web

Ensembl genome browser 2020 edition

http://2020.ensembl.org/

Tags: General, Comparative

Platform: Web

Ensembl genome browser

https://useast.ensembl.org/Homo_sapiens/Location/View?r=17:63992802-64038237

Tags: General, Comparative

Platform: Web, Silo

Biodalliance

http://www.biodalliance.org/

Language: JS

Tags: General, Alignment viewer

Platform: Web

Cylindrical alignment app

https://sourceforge.net/projects/cylindrical-alignment-app/

Alt url https://sourceforge.net/projects/cyl-viewer/

Tags: Exotic

Platform: Desktop

BigTop

https://blog.dnanexus.com/2019-05-21-bigtop-data-visualization/

Tags: Exotic, GWAS

Github: https://github.com/dnanexus/bigtop

Platform: Web

Savant

http://bioinformatics-ca.github.io/savant_genome_browser_lab_2015/

Publication: https://pubmed.ncbi.nlm.nih.gov/22638571/

Language: Java

Tags: General, SV, Alignment viewer

Platform: Desktop

IGV

https://igv.org/

Language: Java

Tags: General, Alignment viewer, SV, Quantitative

Platform: Desktop

IGB

https://bioviz.org/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937187/

Language: Java

Tags: General, Alignment viewer

Platform: Desktop

BasePlayer

https://baseplayer.fi/

Publication: https://www.biorxiv.org/content/10.1101/126482v1.full

Language: Java

Tags: General

Platform: Desktop

wasm bigwig demo browser

https://shk656461.github.io/index.html

Language: WASM

Tags: Special-purpose, Quantitative

Platform: Web

Varsome

https://varsome.com/security-validation/?next=/variant/hg19/NM_000088.3(COL1A1):c.658C%3ET

Tags: Special-purpose, Annotation

Platform: Web, Silo

UGENE

http://ugene.net/

Tags: Special-purpose

Platform: Desktop

Transposcope

https://academic.oup.com/bioinformatics/article-abstract/36/12/3877/5820971?redirectedFrom=fulltext

Language: JS

Tags: Special-purpose, Transposons

Platform: Web

TE-nest

https://pubmed.ncbi.nlm.nih.gov/18032588

Tags: Special-purpose, Transposons, Deadlink?

Note: download link unknown

TASUKE

https://ricegenome.dna.affrc.go.jp/

Tags: Special-purpose, Pangenome

Platform: Web

Staden

https://sourceforge.net/projects/staden/

Tags: Special-purpose, Alignment viewer

Platform: Desktop

SplitThreader

http://splitthreader.com/

Tags: SV, CNV

Github: https://github.com/MariaNattestad/SplitThreader

Platform: Web

SNPViz

http://www.yeastrc.org/snipviz/4.HTML_Config_retrieve_newick_and_fasta_from_server/snip_viz_HTML_config_with_newick_clustering.html

Tags: MSA

Platform: Web

SNPitty

https://bitbucket.org/ccbc/snpitty/src/master/

Publication: https://www.jmdjournal.org/article/S1525-1578(17)30166-6/fulltext

Language: R

Tags: Special-purpose, CNV

Platform: Web

Short read assembly browser

https://rapdb.dna.affrc.go.jp/AssemblyBrowser2/index.html?ref=%22chr01%22&run_id=%22G4toI1%22&start=%22234780%22&end=%22236631%22

Tags: Special-purpose, Alignment viewer

SFARI

https://gene.sfari.org/database/human-gene/

Tags: Special-purpose, CNV

Platform: Web, Silo

SEQing

https://github.com/malewins/SEQing

Language: Python

Tags: Special-purpose

Platform: Web

SeqCover

https://brentp.github.io/seqcover/#gene=AIFM1

Tags: Special-purpose, Coverage

Platform: Web

NGB

https://github.com/epam/NGB

Language: Java

Tags: Special-purpose, Alignment viewer

Platform: Web

MapView

https://sites.google.com/site/wjwdavy/

Publication: https://academic.oup.com/bioinformatics/article/25/12/1554/193807

Tags: Special-purpose, Alignment viewer

Note: links in original paper are dead, but URL provided here works

Platform: Desktop

Panoptes

https://www.malariagen.net/apps/ag1000g/phase1-AR3/index.html

Tags: Special-purpose, Population

Github: https://github.com/cggh/panoptes

LookSeq

https://www.sanger.ac.uk/tool/lookseq/

Tags: Alignment viewer

Platform: Web

Locuszoom

http://locuszoom.org/

Tags: GWAS, Population

Note: Also see locuszoom.js http://locuszoom.org/locuszoomjs.php

Platform: Web

IslandPlot

https://bl.ocks.org/lairdm/c6c235dbfa6e6ee61565

Language: JS

Tags: Special-purpose

Note: D3, SVG

Platform: Web

Introgression browser

https://git.wageningenur.nl/aflit001/ibrowser

Publication: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.12800

Language: Python

Tags: SV, Introgression

Platform: Web

InGAP-SV

http://ingap.sourceforge.net/

Tags: SV, Alignment viewer

Platform: Desktop

Icarus

http://quast.sourceforge.net/icarus.html

Tags: Assembly QC

Platform: Web

Human genome dating

https://human.genome.dating/region/chr1_13250000

Tags: Population, GWAS

Note: made with vega/d3

Platform: Web

Hawkeye

Publication: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-3-r34 (2007)

Tags: Special-purpose, Alignment viewer, Assembly QC

Platform: Desktop

GWAS catalog browser

https://www.ebi.ac.uk/gwas/variants/rs1558902

Tags: Population, LD, GWAS

Platform: Web

GTEX Locus browser

https://gtexportal.org/home/locusBrowserPage/ACTN3

Tags: Expression, Linear, LD

Platform: Web

Gremlin

http://compbio.cs.brown.edu/projects/gremlin/

Tags: SV, Linear

Platform: Web

Gnomad browser

https://github.com/macarthur-lab/gnomadjs

Tags: Special-purpose, Linear, Population

Platform: Web, Silo

Genoverse

https://github.com/wtsi-web/Genoverse

Tags: General, Linear

Platform: Web

GenomeSpy

https://genomespy.app/

Language: JS, WebGL

Tags: CNV, GWAS, Linear, MSA

Platform: Web

Ribbon

http://genomeribbon.com/

Publication: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa680/5885081?redirectedFrom=fulltext

Tags: SV, Alignment viewer

Github: https://github.com/MariaNattestad/ribbon

Platform: Web

Gambit

http://labsergen.langebio.cinvestav.mx/bioinformatics/jacob/?p=473

Tags: Alignment viewer, Linear

Platform: Desktop

EaSeq

https://easeq.net/screenshots/

Publication: https://www.nature.com/articles/nsmb.3180

Tags: Special-purpose, Epigenomics

Platform: Desktop

DNASkittle

https://www.dnaskittle.com/

Tags: Special-purpose

Platform: Web

D3GB

http://d3gb.usal.es/

Language: JS, D3

Tags: Special-purpose

Platform: Web

cnvCurator

http://www.acsu.buffalo.edu/~lm69/cnvCurator

Publication: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0766-y

Language: Java

Tags: CNV, Annotation, Deadlink?

Platform: Desktop

Chromatic

https://chromatic.nci.nih.gov/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5987889/

Language: WASM

Tags: Alignment viewer

Platform: Web

Chopchop

http://chopchop.cbu.uib.no/results/1611256682447.8318/details/9

Tags: Synthetic biology

Apollo aka WebApollo

https://genomearchitect.readthedocs.io/en/latest/

Language: Java, Groovy, JS

Tags: Gene structure, Annotation, JBrowse integration

Platform: Web

Apollo

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151184/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151184/

Language: Java

Tags: Special-purpose, Historical, Deadlink?, Gene structure, Annotation, Comparative

Platform: Desktop

ApE (a plasmid editor)

https://jorgensen.biology.utah.edu/wayned/ape/

Tags: Synthetic biology

Platform: Desktop

seqviz

https://github.com/Lattice-Automation/seqviz#viewer

Tags: Synthetic biology

Platform: Web

OGDRAW

https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

Publication: https://www.biorxiv.org/content/10.1101/545509v1.full.pdf

Tags: Circular, Static

Platform: Web

mummer2circos

https://github.com/metagenlab/mummer2circos

Language: Python

Tags: Static

JupiterPlot

https://github.com/JustinChu/JupiterPlot

Language: Perl

Tags: Circular, Static, Comparative

GenomeProjector

https://github.com/gaou/g-language/wiki

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2636772/

Language: Perl

Tags: Circular, Linear

Platform: Desktop

DNAPlotter

https://www.sanger.ac.uk/science/tools/dnaplotter

Language: Java

Tags: Circular

Platform: Desktop

CircosJS

https://github.com/nicgirault/circosJS

Language: JS

Tags: Circular

Platform: Web

Circleator

http://jonathancrabtree.github.io/Circleator/index.html

Language: Perl

Tags: Circular, Static

Circa

https://omgenomics.com/circa

Tags: Commercial, Circular

Platform: Desktop

BioCircos.js

http://bioinfo.ibp.ac.cn/biocircos/

Language: JS

Tags: Circular

Platform: Web

VizAln (from HipSTR)

https://github.com/tfwillems/HipSTR

Tags: Text based

SvABA

https://github.com/walaj/svaba#alignmentstxtgz

Tags: Text based

Platform: CLI

Samtools tview

http://www.htslib.org/

Language: C

Tags: Text based, Alignment viewer

Platform: CLI

Samtools depth visualization

https://twitter.com/yokofakun/status/1178686978541441025

Tags: Text based, Coverage

Platform: CLI, GNUplot

Rna Alignment Viewers

http://biowiki.org/wiki/index.php?title=Rna_Alignment_Viewers&redirect=no

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109877/

Language: Perl

Tags: Text based

Platform: CLI

pyBamView

https://mgymrek.github.io/pybamview/

Language: Python

Tags: Alignment viewer, Static

Note: See supplementary info for more figures, supports padded SAM/BAM which is fairly rare

Platform: CLI

plotReads

http://campuspress.yale.edu/knightlab/ruddle/plotreads/

Tags: Text based

Platform: CLI, Static

Hapviz

https://github.com/ekg/hapviz

Language: C

Tags: Text based

Platform: CLI

Bamcov

https://github.com/fbreitwieser/bamcov

Language: C

Tags: Text based, Coverage

Platform: CLI

ASCIIGenome

https://github.com/dariober/ASCIIGenome

Language: Java

Tags: Text based, Alignment viewer

Platform: CLI

Alv

https://github.com/arvestad/alv

Language: Python

Tags: Text based, MSA

Platform: CLI

Alan

https://github.com/mpdunne/alan

Language: Bash

Tags: Text based, MSA

Platform: CLI

sequence tube map

https://github.com/vgteam/sequenceTubeMap

Language: JS

Tags: Graph

Platform: Web

odgi draw + odgi viz

https://odgi.readthedocs.io/en/latest/index.html

Tags: Graph

Note: Example from https://github.com/pangenome/pggb

MoMi-G

https://github.com/MoMI-G/MoMI-G/

Language: JS

Tags: Graph, Multi, Alignment viewer, Circular, SV

Platform: Web

graphgenomeviewer

https://cmdcolin.github.io/graphgenomeviewer/

Language: JS

Tags: Graph

Platform: Web

gGnomes.js

https://github.com/mskilab/gGnome.js

Language: JS

Tags: SV, CNV, Breakends, Graph

Platform: Web

gfaestus

https://github.com/chfi/gfaestus

Language: Rust

Tags: Graph

Note: See demo video displaying GFF3 annotations on graph https://www.youtube.com/watch?v=A-HnKXIrJl4

Bandage

https://github.com/rrwick/Bandage/

Publication: https://academic.oup.com/bioinformatics/article/31/20/3350/196114

Language: C++

Tags: Graph

Platform: Desktop

XMatchView

https://www.bcgsc.ca/resources/software/xmatchview

Tags: Comparative

Platform: Desktop

VISTA browser

http://pipeline.lbl.gov/cgi-bin/gateway2

Tags: Comparative

Platform: Web, Silo

Tripal MapViewer

https://academic.oup.com/database/article/doi/10.1093/database/baz100/5612723

Tags: Comparative, Ideogram

SynVisio

https://synvisio.github.io/

Language: JS

Tags: Comparative, Linear, Dotplot

SynTView

http://hub18.hosting.pasteur.fr/SynTView/documentation/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849071/

Tags: Comparative, Dotplot, Linear

Platform: Desktop, Web, Flash

Synteny browser

https://github.com/TheJacksonLaboratory/syntenybrowser

Tags: Comparative

Platform: Web

Synima

https://github.com/rhysf/Synima

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5697234/

Language: Perl

Tags: Comparative

Platform: CLI

SyMap

http://www.agcol.arizona.edu/software/symap/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105427/

Tags: Comparative, Dotplot, Linear

Platform: Desktop

progressiveMauve viewer

http://darlinglab.org/mauve/user-guide/viewer.html

Tags: Comparative

Platform: Desktop

syri/plotsr

https://schneebergerlab.github.io/syri/plotsr.html

Language: Python

Tags: Comparative, Linear

Parasight

https://baileylab.brown.edu/parasight/galframe.html

Language: Perl

Tags: Comparative

Note: Examples at https://ratparalogy.gs.washington.edu/

pafr

https://github.com/dwinter/pafr

Language: R

Tags: Comparative, Dotplot, Linear

OMA local synteny browser

https://omabrowser.org/oma/synteny/ADH1A_HUMAN/

Tags: Comparative, Gene order

Platform: Web, Silo

Multiple genome viewer

http://www.informatics.jax.org/mgv/

Tags: Comparative

Platform: Web, Silo

MizBee

http://www.cs.utah.edu/~miriah/mizbee/Overview.html

Publication: https://ieeexplore.ieee.org/document/5290692

Language: Processing

Tags: Comparative

Platform: Desktop

MCScanX

https://github.com/wyp1125/MCScanX

Language: Perl

Tags: Comparative, Dotplot, Circular, Linear, Ideogram

Platform: CLI

MCScan (python version)

https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)

Language: Python

Tags: Comparative, Dotplot, Linear

Platform: CLI

mauve-viewer

https://github.com/nconrad/mauve-viewer

Language: JS

Tags: Comparative

Platform: Web

GIVE

https://zhong-lab-ucsd.github.io/GIVE_homepage/

Language: JS

Tags: Comparative, Linear, Quantitative

Platform: Web

gggenomes

https://github.com/thackl/gggenomes

Language: R

Tags: Comparative

Platform: Package

Genomicus

https://www.genomicus.biologie.ens.fr/genomicus/

Tags: Comparative, Ideogram, Dotplot

Platform: Web, Silo

Genome-plots-processing

https://github.com/filip-husnik/genome-plots-processing

Language: Processing

Tags: Comparative

Genome Context Viewer

https://www.legumefederation.org/gcv/phytozome_10_2/

Tags: Comparative, Gene order

Platform: Web, Silo

GBrowse_syn

http://gmod.org/wiki/GBrowse_syn

Language: Perl

Tags: Comparative

Platform: Web

Edinburgh-Genome-Foundry/DnaFeaturesViewer

https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer

Publication: https://academic.oup.com/bioinformatics/article-abstract/36/15/4350/5868559?redirectedFrom=PDF

Language: Python

Tags: Microbiology, Synthetic biology

Platform: Desktop

EasyFig

https://mjsull.github.io/Easyfig/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065679/

Language: Python

Tags: Comparative

Platform: CLI

Cvit.js

https://github.com/LegumeFederation/cvitjs

Tags: Comparative

Platform: Web

CVit

https://sourceforge.net/projects/cvit/

Language: Perl

Tags: Comparative

Platform: Web

CrossBrowse

https://github.com/shenkers/CrossBrowse

Publication: https://www.biorxiv.org/content/10.1101/272880v1.full

Language: Java

Tags: Comparative

Platform: Desktop

Comparative assembly hub / "snake track"

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145/

Tags: Comparative, UCSC integration

Platform: Web

CoGe

https://genomevolution.org/coge/

Language: Perl

Tags: Comparative, Dotplot, Linear, JBrowse integration

Platform: Web, Silo

CMap

http://gmod.org/wiki/CMap

Language: Perl

Tags: Comparative

Platform: Web

Chromatiblock

https://github.com/mjsull/chromatiblock

Publication: https://www.biorxiv.org/content/10.1101/800920v2.full.pdf

Language: Python

Tags: Comparative, Pangenome

Platform: Web

Biodalliance comparative demo

http://biodalliance.org/dev/test-comparative.html

Language: JS

Tags: Comparative

Platform: Web

Artemis comparison tool (ACT)

https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

Language: Java

Tags: Comparative

Platform: Desktop

AliTV

https://alitvteam.github.io/AliTV/d3/AliTV.html

Tags: Comparative

Platform: Web

Aequatus

https://github.com/TGAC/Aequatus

Tags: Comparative, Deadlink?

Platform: Web, Silo

trackViewer

https://bioconductor.org/packages/release/bioc/vignettes/trackViewer/inst/doc/trackViewer.html

Language: R

Tags: Static, Lollipops, Quantitative

TnT

https://tnt.marlin.pub/articles/introduction

Language: R, JS

Tags: Gene structure

Platform: Web, Interactive

svviz2

https://github.com/nspies/svviz2

Publication: https://pubmed.ncbi.nlm.nih.gov/26286809/

Language: Python

Tags: Static, SV, Insertion

svviz

https://github.com/svviz/svviz

Publication: https://pubmed.ncbi.nlm.nih.gov/26286809/

Language: Python

Tags: Static, SV, Insertion

svv

https://github.com/ryanlayer/svv

Language: Python

Tags: Static, SV, Coverage

svist4get

https://link.springer.com/article/10.1186/s12859-019-2706-8

Publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2706-8

Language: Python

Tags: Static

Sushi

https://www.bioconductor.org/packages/release/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

Language: R

Tags: Static, Multi

Spliceclust

https://github.com/pkimes/spliceclust

Language: R

Tags: Static, Splicing

SparK

https://github.com/harbourlab/SparK

Publication: https://www.biorxiv.org/content/10.1101/845529v1.full.pdf

Language: Python

Tags: Static, Hi-C, Quantitative

shinyChromosome

http://150.109.59.144:3838/shinyChromosome/

Publication: https://www.sciencedirect.com/science/article/pii/S1672022919301883

Language: R, Shiny

Tags: Dotplot, Linear, Ideogram

Platform: Web

shabam

https://github.com/dlrice/shabam

Language: Python

Tags: Static

SashimiPlot

https://miso.readthedocs.io/en/fastmiso/sashimi.html

Language: Python

Tags: Static, Expression, Splicing

Samplot

https://github.com/ryanlayer/samplot

Language: Python

Tags: Static, SV, Alignment viewer

RepViz

https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4473-z

Language: R

Tags: Static, Quantitative

Github: https://github.com/elolab/RepViz

RACER

https://oliviasabik.github.io/RACERweb/articles/IntroToRACER.html

Language: R

Tags: Static, GWAS

pyGenomeTracks

https://github.com/deeptools/pyGenomeTracks

Language: Python

Tags: Static, Hi-C

PureScript genetics browser

https://github.com/chfi/purescript-genetics-browser

Language: Purescript

Tags: GWAS

Platform: Web

pauvre

https://github.com/conchoecia/pauvre

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991124/figure/fig-3/

Language: Python

Tags: Static, Misc QC, Comparative

Platform: CLI

Pairoscope

http://pairoscope.sourceforge.net/

Language: C++

Tags: Static, SV

Millefy

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7053140/

Language: R

Tags: Single cell

Platform: Package

Methplotlib

https://www.biorxiv.org/content/10.1101/826107v1.full.pdf

Language: Python

Tags: Static, Epigenomics, Methylation

Mason

http://www.yeastrc.org/mason/

Tags: Static, Protein

Platform: Web

Lollipops

https://github.com/joiningdata/lollipops

Language: Go

Tags: Static, Protein, Lollipops

JVarKit/BamToSVG

http://lindenb.github.io/jvarkit/BamToSVG.html

Language: Java

Tags: Static, Alignment viewer

HiCPlotter

https://github.com/kcakdemir/HiCPlotter

Language: Python

Tags: Static, Hi-C

Hagfish

https://github.com/mfiers/hagfish/wiki/Plots

Language: Python

Tags: Static, Coverage

Gviz

https://bioconductor.org/packages/release/bioc/html/Gviz.html

Language: R

Tags: Static, Alignment viewer, Quantitative, Multi

gtrellis

http://bioconductor.org/packages/devel/bioc/vignettes/gtrellis/inst/doc/gtrellis.html

Language: R

Tags: Static, Ideogram, Quantitative, CNV

GSSPlayground

https://github.com/orangeSi/GSSplayground

Language: Perl

Tags: Comparative, Static, Alignment viewer

GGsashimi

https://github.com/guigolab/ggsashimi

Language: R

Tags: Static

GGgenes

https://github.com/wilkox/gggenes

Language: R

Tags: Static, Comparative

ggbio

http://www.bioconductor.org/packages/2.11/bioc/vignettes/ggbio/inst/doc/ggbio.pdf

Publication: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-8-r77

Language: R

Tags: Static, Ideogram, Circular, Multi

genoPlotR

http://genoplotr.r-forge.r-project.org/

Language: R

Tags: Static, Comparative

GenomeView (java app)

https://genomeview.org/content/quick-start-guide

Language: Java

Tags: Alignment viewer

GenomeView

https://github.com/nspies/genomeview

Language: Python

Tags: Static, SV, Alignment viewer

GenomeTools

http://genometools.org/

Language: C

Tags: Static, Gene structure

Genome STRiP

http://software.broadinstitute.org/software/genomestrip/

Tags: Static

Geneviz

https://jrderuiter.github.io/geneviz/usage.html

Language: R

Tags: Static, Gene structure

FeatureViewer

https://github.com/calipho-sib/feature-viewer

Tags: Static, Gene structure

Platform: Web

ExonIntron

http://wormweb.org/exonintron

Tags: Static, Gene structure

DNAPlotLib

https://github.com/VoigtLab/dnaplotlib

Language: Python

Tags: Static, Synthetic biology

CNVpytor

https://github.com/abyzovlab/CNVpytor

Language: Python

Tags: Static, CNV

CNVPlot

https://github.com/dantaki/CNVplot/

Language: R

Tags: Static, CNV

CNView

https://github.com/RCollins13/CNView

Language: R

Tags: Static, CNV

Chimeraviz

https://github.com/stianlagstad/chimeraviz

Language: R

Tags: Gene fusion, Circular, Linear

ChIA-Pipe

https://github.com/TheJacksonLaboratory/ChIA-PIPE

Publication: https://www.biorxiv.org/content/10.1101/506683v1.full.pdf

Tags: Static, Epigenomics

BAMSnap

https://github.com/parklab/bamsnap

Language: Python

Tags: Static, Alignment viewer

BAMScale

https://github.com/ncbi/BAMscale

Publication: https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-020-00343-x

Language: C, R

Tags: CNV, Static

CNVkit

https://cnvkit.readthedocs.io/en/stable/plots.html

Publication: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004873

Language: Python

Tags: CNV

Github: https://github.com/etal/cnvkit

aCNVViewer

https://github.com/FJD-CEPH/aCNViewer

Publication: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0189334

Language: Python

Tags: CNV, Static

Wasabi

http://wasabiapp.org/

Tags: MSA

Platform: Web

TeXShade

http://mirrors.ibiblio.org/CTAN/macros/latex/contrib/texshade/texshade.pdf

Tags: MSA

Platform: Desktop

STRAP

http://www.bioinformatics.org/strap/

Tags: MSA

Note: also see AA

Platform: Web, Applet

seqotron

https://github.com/4ment/seqotron

Language: Objective-C

Tags: MSA

Platform: Desktop

react-msaview

https://github.com/GMOD/react-msaview

Language: JS, React

Tags: MSA

React MSAViewer

https://github.com/plotly/react-msa-viewer

Language: JS, React

Tags: MSA

Platform: Web

pymsaplotter

https://github.com/orangeSi/pymsaploter

Language: Python

Tags: MSA

pyBoxshade

https://github.com/mdbaron42/pyBoxshade

Language: Python

Tags: MSA

Note: also see boxshade

Platform: Desktop

NCBI MSA Viewer

https://www.ncbi.nlm.nih.gov/projects/msaviewer/

Tags: MSA

Platform: Web, CGI

MView

https://www.ebi.ac.uk/Tools/msa/mview/

Tags: MSA

Platform: Web

msaR

https://github.com/zachcp/msaR

Language: R, JS

Tags: MSA

Note: uses BioJS/MSA

Platform: Desktop, R/htmlwidget

MSABrowser

https://thekaplanlab.github.io/

Tags: MSA

Platform: Web

LogoJS

https://logojs.wenglab.org/app/gallery/

Language: JS

Tags: Logo

Platform: Web

JSAV

http://www.bioinf.org.uk/software/jsav

Publication: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304231/

Language: JS

Tags: MSA

Platform: Web

Jalview

https://www.jalview.org/

Language: Java

Tags: MSA

Platform: Desktop

ESPript

http://espript.ibcp.fr/ESPript/ESPript/

Tags: MSA

Platform: Desktop

Boxshade

https://embnet.vital-it.ch/software/BOX_form.html

Tags: MSA

Platform: Web

BioJS/MSA

https://msa.biojs.net/

Publication: https://academic.oup.com/bioinformatics/article/32/22/3501/2525598?login=true

Tags: MSA

Platform: Web

AliView

http://www.ormbunkar.se/aliview/

Language: Java

Tags: MSA

Platform: Desktop

AlignmentViewer

https://alignmentviewer.org/

Tags: MSA

Platform: Web

AlignmentComparator

http://bioinfweb.info/AlignmentComparator/

Language: Java

Tags: MSA

Note: Uses http://bioinfweb.info/LibrAlign/

alignment.js

https://github.com/veg/alignment.js

Tags: MSA

Platform: Web

abrowse

https://github.com/ihh/abrowse

Tags: MSA

Platform: Web

AA

http://www.bioinformatics.org/strap/aa

Tags: MSA

Note: also see STRAP

Platform: Web

Bionano

https://bionanogenomics.com/technology/structural-variation/

Tags: Commercial, SV

Strand NGS

https://www.strand-ngs.com/

Tags: Commercial

SnapGene

https://www.snapgene.com/

Tags: Commercial

Persephone

https://persephonesoft.com/

Tags: Commercial, Comparative

MacVector

https://macvector.com/

Tags: Commercial

Lucid viewer

https://lucidalign.com/

Tags: Commercial

Golden Helix

http://goldenhelix.com/GenomeBrowse/

Tags: Commercial

Genestack

https://genestack.com/blog/2015/05/28/navigation-in-genestack-genome-browser/

Tags: Commercial

Geneious

https://www.geneious.com/

Tags: Commercial, Synthetic biology

DNASTAR

https://www.dnastar.com/

Tags: Commercial

CLC Genomics workbench

https://digitalinsights.qiagen.com/news/blog/discovery/structural-variant-detection-using-clc-genomics-workbench/

Tags: Commercial, SV

Benchling

https://www.benchling.com/

Tags: Commercial, Synthetic biology

ATCC Genome Portal (American Type Culture Collection)

https://docs.onecodex.com/en/articles/3996697-using-the-genome-browser

Tags: Commercial, Microbiology

Alamut

https://www.interactive-biosoftware.com/alamut-visual/

Tags: Commercial

10x genomics/Loupe

https://support.10xgenomics.com/genome-exome/software/visualization/latest/structural-variants

Tags: Commercial

Note: if you would like your tool removed or screenshot removed (for copyright purposes for example) let me know

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