awesome-genome-visualization

awesome-genome-visualization

This is a companion website for the github repo https://github.com/cmdcolin/awesome-genome-visualization

Also check out our twitter account @awesomegenomev1

Feel free to submit PRs to add more tools

Filters:




Before clicking these sort routines: Try to avoid being unfairly biased by citation numbers and github stars!! Best effort was made to find the right DOI and github repo

Sorts:

Selection:

AA (alignment annotator)

Publication: (doi link) (2014) (# citations 45)

Language: JS

Tags: MSA

Note: also see STRAP

Platform: Web

screenshot of AA (alignment annotator)

abrowse

Language: JS

Tags: MSA

Github Stargazers: 10

Platform: Web

screenshot of abrowse

alignment.js

Language: JS

Tags: MSA

Github Stargazers: 7

Platform: Web

screenshot of alignment.js

AlignmentComparator

Language: Java

Tags: MSA

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

Github Stargazers: 1

screenshot of AlignmentComparator

AlignmentViewer

Publication: (direct link) (doi link) (2020) (# citations 3)

Language: JS

Tags: MSA

Github Stargazers: 15

Platform: Web

screenshot of AlignmentViewer

AliView

Publication: (doi link) (2014) (# citations 1468)

Language: Java

Tags: MSA

Github Stargazers: 90

Platform: Desktop

screenshot of AliView

BioJS/MSA

Publication: (direct link) (doi link) (2016) (# citations 59)

Language: JS

Tags: MSA

Github Stargazers: 163

Platform: Web

screenshot of BioJS/MSA

Boxshade

Publication: (direct link) (doi link) (2000) (# citations 4)

Tags: MSA, Deadlink

Note: Also available as a command line tool with `apt install boxshade`. See also rMSA which can automate running boxshade from within R

Platform: Web, CLI

screenshot of Boxshade

ESPript

Publication: (doi link) (1999) (# citations 2286)

Tags: MSA

Note: Primarily a web interface but can download a binary for linux https://espript.ibcp.fr/ESPript/ESPript/esp_faq.php

Platform: Web, CLI

screenshot of ESPript

Jalview

Publication: (doi link) (2009) (# citations 5912)

Language: Java

Tags: MSA

Platform: Desktop

screenshot of Jalview

JSAV

Publication: (direct link) (doi link) (2014) (# citations 14)

Language: JS

Tags: MSA

Github Stargazers: 8

Platform: Web

screenshot of JSAV

LogoJS

Publication: (doi link) (2020) (# citations 2)

Language: JS

Tags: Logo

Github Stargazers: 11

Platform: Web

screenshot of LogoJS

MSABrowser

Publication: (doi link) (2021) (# citations 1)

Language: JS

Tags: MSA

Github Stargazers: 20

Platform: Web

screenshot of MSABrowser

msaR

Language: R, JS

Tags: MSA

Note: uses BioJS/MSA

Github Stargazers: 6

Platform: Desktop, R/htmlwidget

screenshot of msaR

MView

Publication: (doi link) (1998) (# citations 236)

Tags: MSA

Note: See also their web versions of clustal omega etc. which have similar outputs

Platform: Web, Silo

screenshot of MView

pyBoxshade

Language: Python

Tags: MSA

Note: also see boxshade

Github Stargazers: 10

Platform: Desktop

screenshot of pyBoxshade

pymsaplotter

Language: Python

Tags: MSA

Github Stargazers: 7

screenshot of pymsaplotter

React MSAViewer

Language: JS, React

Tags: MSA

Github Stargazers: 17

Platform: Web

screenshot of React MSAViewer

react-msaview

Language: JS, React

Tags: MSA

Github Stargazers: 5

screenshot of react-msaview

seqotron

Publication: (doi link) (2016) (# citations 28)

Language: Objective-C

Tags: MSA

Github Stargazers: 26

Platform: Desktop

screenshot of seqotron

STRAP

Publication: (doi link) (2014) (# citations 45)

Tags: MSA

Note: also see AA

Platform: Web, Applet

screenshot of STRAP

Wasabi

Publication: (doi link) (2015) (# citations 41)

Language: JS, Python

Tags: MSA

Github Stargazers: 17

Platform: Web

screenshot of Wasabi

aCNVViewer

Publication: (direct link) (doi link) (2017) (# citations 3)

Language: Python

Tags: CNV, Static

Github Stargazers: 18

screenshot of aCNVViewer

CNVkit

Publication: (direct link) (doi link) (2016) (# citations 802)

Language: Python

Tags: CNV

Github Stargazers: 353

screenshot of CNVkit

BAMScale

Publication: (direct link) (doi link) (2020) (# citations 14)

Language: C, R

Tags: CNV, Static

Github Stargazers: 55

screenshot of BAMScale

BAMSnap

Publication: (doi link) (2021) (# citations 1)

Language: Python

Tags: Static, Alignment viewer

Github Stargazers: 87

screenshot of BAMSnap

ChIA-Pipe

Publication: (direct link) (doi link) (2020) (# citations 6)

Tags: Static, Epigenomics

Github Stargazers: 19

screenshot of ChIA-Pipe

Chimeraviz

Publication: (doi link) (2017) (# citations 19)

Language: R

Tags: Gene fusion, Circular, Linear

Github Stargazers: 28

screenshot of Chimeraviz

CNView

Publication: (doi link) (2016) (# citations 7)

Language: R

Tags: Static, CNV

Github Stargazers: 61

screenshot of CNView

CNVPlot

Publication: (doi link) (2015) (# citations 0)

Language: R

Tags: Static, CNV

Github Stargazers: 14

screenshot of CNVPlot

CNVpytor

Publication: (doi link) (2021) (# citations 7)

Language: Python

Tags: Static, CNV

Github Stargazers: 82

screenshot of CNVpytor

DNAPlotLib

Publication: (doi link) (2016) (# citations 41)

Language: Python

Tags: Static, Synthetic biology

Github Stargazers: 249

screenshot of DNAPlotLib

GenomeTools

Publication: (doi link) (2013) (# citations 245)

Language: C

Tags: Static, Gene structure

Github Stargazers: 230

screenshot of GenomeTools

GenomeView

Publication: (doi link) (2018) (# citations 2)

Language: Python

Tags: Static, SV, Alignment viewer

Github Stargazers: 120

screenshot of GenomeView

genoPlotR

Publication: (doi link) (2010) (# citations 446)

Language: R

Tags: Static, Comparative

screenshot of genoPlotR

GGgenes

Language: R, ggplot2

Tags: Static, Comparative

Github Stargazers: 304

screenshot of GGgenes

GGsashimi

Publication: (doi link) (2018) (# citations 89)

Language: R, ggplot2

Tags: Static

Github Stargazers: 83

screenshot of GGsashimi

HiCPlotter

Publication: (doi link) (2015) (# citations 123)

Language: Python

Tags: Static, Hi-C

Github Stargazers: 6

screenshot of HiCPlotter

Methplotlib

Publication: (doi link) (2020) (# citations 19)

Language: Python

Tags: Static, Epigenomics, Methylation

Github Stargazers: 67

screenshot of Methplotlib

Millefy

Publication: (doi link) (2020) (# citations 3)

Language: R

Tags: Single cell

Github Stargazers: 21

Platform: Package

screenshot of Millefy

pauvre

Publication: (doi link) (2020) (# citations 7)

Language: Python

Tags: Static, Misc QC, Comparative

Github Stargazers: 41

Platform: CLI

screenshot of pauvre

PureScript genetics browser

Language: Purescript

Tags: GWAS

Github Stargazers: 5

Platform: Web

screenshot of PureScript genetics browser

pyGenomeTracks

Publication: (doi link) (2020) (# citations 77)

Language: Python

Tags: Static, Hi-C

Github Stargazers: 578

screenshot of pyGenomeTracks

RACER

Publication: (doi link) (2018) (# citations 3)

Language: R

Tags: Static, GWAS

Github Stargazers: 11

screenshot of RACER

Samplot

Publication: (doi link) (2021) (# citations 12)

Language: Python

Tags: Static, SV, Alignment viewer

Github Stargazers: 366

screenshot of Samplot

SashimiPlot

Publication: (doi link) (2015) (# citations 105)

Language: Python

Tags: Static, Expression, Splicing

Github Stargazers: 124

screenshot of SashimiPlot

shabam

Language: Python

Tags: Static

Github Stargazers: 6

screenshot of shabam

shinyChromosome

Publication: (direct link) (doi link) (2019) (# citations 10)

Language: R, Shiny

Tags: Dotplot, Linear, Ideogram

Github Stargazers: 35

Platform: Web

screenshot of shinyChromosome

SparK

Publication: (direct link) (doi link) (2019) (# citations 14)

Language: Python

Tags: Static, Hi-C, Quantitative

Github Stargazers: 82

screenshot of SparK

svist4get

Publication: (doi link) (2019) (# citations 24)

Language: Python

Tags: Static

screenshot of svist4get

svv

Language: Python

Tags: Static, SV, Coverage

Github Stargazers: 25

screenshot of svv

svviz

Publication: (doi link) (2015) (# citations 14)

Language: Python

Tags: Static, SV, Insertion

Github Stargazers: 74

screenshot of svviz

svviz2

Publication: (doi link) (2015) (# citations 14)

Language: Python

Tags: Static, SV, Insertion

Github Stargazers: 35

screenshot of svviz2

TnT

Publication: (doi link) (2016) (# citations 3)

Language: R, JS

Tags: Gene structure

Github Stargazers: 16

Platform: Web, Interactive

screenshot of TnT

Aequatus

Publication: (doi link) (2018) (# citations 1)

Language: JS, Java

Tags: Comparative, Deadlink?

Github Stargazers: 7

Platform: Web, Silo

screenshot of Aequatus

AliTV

Publication: (doi link) (2017) (# citations 39)

Language: JS, D3, Perl

Tags: Comparative

Platform: Web

screenshot of AliTV

Artemis comparison tool (ACT)

Publication: (doi link) (2005) (# citations 1259)

Language: Java

Tags: Comparative

Github Stargazers: 171

Platform: Desktop

screenshot of Artemis comparison tool (ACT)

Biodalliance comparative demo

Publication: (doi link) (2011) (# citations 87)

Language: JS

Tags: Comparative

Github Stargazers: 217

Platform: Web

screenshot of Biodalliance comparative demo

Chromatiblock

Publication: (direct link) (doi link) (2020) (# citations 1)

Language: Python

Tags: Comparative, Pangenome, Microbiology

Github Stargazers: 21

Platform: Web

screenshot of Chromatiblock

CMap

Publication: (doi link) (2009) (# citations 63)

Language: Perl

Tags: Comparative

Github Stargazers: 4

Platform: Web

screenshot of CMap

CoGe

Publication: (doi link) (2017) (# citations 77)

Language: Perl

Tags: Comparative, Dotplot, Linear, JBrowse integration

Github Stargazers: 41

Platform: Web, Silo

screenshot of CoGe

CrossBrowse

Publication: (direct link) (doi link) (2018) (# citations 0)

Language: Java

Tags: Comparative

Github Stargazers: 9

Platform: Desktop

screenshot of CrossBrowse

CVit

Publication: (doi link) (2011) (# citations 23)

Language: Perl

Tags: Comparative, Ideogram

Github Stargazers: 1

Platform: Web

screenshot of CVit

Cvit.js

Language: JS

Tags: Comparative, Ideogram

Github Stargazers: 10

Platform: Web

screenshot of Cvit.js

EasyFig

Publication: (direct link) (doi link) (2011) (# citations 1779)

Language: Python

Tags: Comparative

Github Stargazers: 63

Platform: CLI

screenshot of EasyFig

GBrowse_syn

Publication: (doi link) (2010) (# citations 29)

Language: Perl

Tags: Comparative

Github Stargazers: 46

Platform: Web

screenshot of GBrowse_syn

Genome Context Viewer

Publication: (doi link) (2017) (# citations 17)

Language: JS, Typescript

Tags: Comparative, Gene order

Github Stargazers: 20

Platform: Web, Silo

screenshot of Genome Context Viewer

Genomicus

Publication: (doi link) (2021) (# citations 5)

Tags: Comparative, Ideogram, Dotplot

Platform: Web, Silo

screenshot of Genomicus

gggenomes

Publication: (doi link) (2020) (# citations 1)

Language: R

Tags: Comparative

Github Stargazers: 335

Platform: Package

screenshot of gggenomes

mauve-viewer

Language: JS

Tags: Comparative

Github Stargazers: 28

Platform: Web

screenshot of mauve-viewer

MCScan (python version)

Publication: (doi link) (2015) (# citations 252)

Language: Python

Tags: Comparative, Dotplot, Linear

Github Stargazers: 518

Platform: CLI

screenshot of MCScan (python version)

MCScanX

Publication: (doi link) (2012) (# citations 2151)

Language: Perl

Tags: Comparative, Dotplot, Circular, Linear, Ideogram

Github Stargazers: 128

Platform: CLI

screenshot of MCScanX

mGSV (multiple genome synteny viewer)

Publication: (doi link) (2012) (# citations 17)

Tags: Comparative, Deadlink?

Github Stargazers: 5

Platform: Web, Silo

screenshot of mGSV (multiple genome synteny viewer)

MizBee

Publication: (direct link) (doi link) (2009) (# citations 102)

Language: Processing

Tags: Comparative

Platform: Desktop

screenshot of MizBee

Multiple genome viewer

Publication: (doi link) (2021) (# citations 1)

Language: JS, VueJS

Tags: Comparative

Github Stargazers: 7

Platform: Web, Silo

screenshot of Multiple genome viewer

pafr

Language: R, ggplot2

Tags: Comparative, Dotplot, Linear

Github Stargazers: 46

screenshot of pafr

Parasight

Publication: (doi link) (2005) (# citations 713)

Language: Perl

Tags: Comparative

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

screenshot of Parasight

SyMap

Publication: (doi link) (2006) (# citations 134)

Tags: Comparative, Dotplot, Linear

Platform: Desktop

screenshot of SyMap

Synima

Publication: (doi link) (2017) (# citations 30)

Language: Perl

Tags: Comparative

Github Stargazers: 49

Platform: CLI

screenshot of Synima

Tripal MapViewer

Publication: (doi link) (2019) (# citations 3)

Tags: Comparative, Ideogram

Github Stargazers: 1

screenshot of Tripal MapViewer

VISTA browser

Publication: (doi link) (2004) (# citations 1354)

Tags: Comparative

Platform: Web, Silo

screenshot of VISTA browser

XMatchView

Publication: (doi link) (2018) (# citations 2)

Language: Python

Tags: Comparative

Github Stargazers: 34

Platform: Desktop

screenshot of XMatchView

AGB assembly graph browser

Publication: (direct link) (doi link) (2019) (# citations 10)

Language: Python

Tags: Graph

Github Stargazers: 61

Platform: Web

No screenshot

Bandage

Publication: (direct link) (doi link) (2015) (# citations 946)

Language: C++

Tags: Graph

Note: See also BandageNG https://github.com/asl/BandageNG

Github Stargazers: 448

Platform: Desktop

screenshot of Bandage

gfaestus

Language: Rust

Tags: Graph

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

Github Stargazers: 35

screenshot of gfaestus

gGnomes

Language: R

Tags: SV, CNV, Breakends, Graph

Github Stargazers: 22

Platform: Web

screenshot of gGnomes

gGnomes.js

Language: JS

Tags: SV, CNV, Breakends, Graph

Github Stargazers: 19

Platform: Web

screenshot of gGnomes.js

MoMi-G

Publication: (doi link) (2019) (# citations 13)

Language: JS

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

Github Stargazers: 71

Platform: Web

screenshot of MoMi-G

odgi draw + odgi viz + odgi inject

Publication: (doi link) (2021) (# citations 9)

Language: C++

Tags: Graph

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

Github Stargazers: 116

screenshot of odgi draw + odgi viz + odgi inject

sequence tube map

Publication: (doi link) (2019) (# citations 18)

Language: JS

Tags: Graph

Github Stargazers: 118

Platform: Web

screenshot of sequence tube map

Alan

Language: Bash

Tags: Text based, MSA

Github Stargazers: 73

Platform: CLI

screenshot of Alan

Alv

Publication: (doi link) (2018) (# citations 2)

Language: Python

Tags: Text based, MSA

Github Stargazers: 74

Platform: CLI

screenshot of Alv

ASCIIGenome

Publication: (doi link) (2017) (# citations 1)

Language: Java

Tags: Text based, Alignment viewer

Github Stargazers: 181

Platform: CLI

screenshot of ASCIIGenome

Bamcov

Language: C

Tags: Text based, Coverage

Github Stargazers: 89

Platform: CLI

screenshot of Bamcov

Hapviz

Language: C

Tags: Text based

Github Stargazers: 11

Platform: CLI

screenshot of Hapviz

pyBamView

Publication: (doi link) (2014) (# citations 4)

Language: Python

Tags: Alignment viewer, Static

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

Platform: CLI

screenshot of pyBamView

Sam2pairwise

Publication: (doi link)

Language: C++

Tags: Text based

Github Stargazers: 28

Platform: CLI

No screenshot

Samtools tview

Publication: (doi link) (2009) (# citations 35044)

Language: C

Tags: Text based, Alignment viewer

Github Stargazers: 1226

Platform: CLI

screenshot of Samtools tview

SvABA

Publication: (doi link) (2018) (# citations 183)

Tags: Text based

Github Stargazers: 179

Platform: CLI

screenshot of SvABA

VizAln (from HipSTR)

Publication: (doi link) (2017) (# citations 133)

Tags: Text based

Github Stargazers: 74

screenshot of VizAln (from HipSTR)

Anvio

Publication: (doi link) (2015) (# citations 961)

Language: Python

Tags: Circular

Github Stargazers: 346

No screenshot

BioCircos.js

Publication: (doi link) (2016) (# citations 76)

Language: JS

Tags: Circular

Platform: Web

screenshot of BioCircos.js

circlize

Publication: (doi link) (2014) (# citations 1511)

Language: R

Tags: Circular, Static

Github Stargazers: 797

screenshot of circlize

Circos

Publication: (doi link) (2009) (# citations 6405)

Language: Perl

Tags: Circular, Static

Note: the github repo is not up to date with the latest code

Github Stargazers: 57

screenshot of Circos

CircosJS

Language: JS

Tags: Circular

Github Stargazers: 457

Platform: Web

screenshot of CircosJS

DNAPlotter

Publication: (doi link) (2008) (# citations 609)

Language: Java

Tags: Circular

Platform: Desktop

screenshot of DNAPlotter

GenomeProjector

Publication: (direct link) (doi link) (2009) (# citations 31)

Language: Perl

Tags: Circular, Linear

Platform: Desktop

screenshot of GenomeProjector

JupiterPlot

Publication: (doi link)

Language: Perl

Tags: Circular, Static, Comparative

Github Stargazers: 51

screenshot of JupiterPlot

mummer2circos

Language: Python

Tags: Static

Github Stargazers: 56

screenshot of mummer2circos

OGDRAW

Publication: (doi link) (2019) (# citations 501)

Tags: Circular, Static

Platform: Web

screenshot of OGDRAW

Apollo aka WebApollo

Publication: (doi link) (2013) (# citations 282)

Language: Java, Groovy, JS

Tags: Gene structure, Annotation, JBrowse integration

Github Stargazers: 105

Platform: Web

screenshot of Apollo aka WebApollo

Chopchop

Publication: (doi link) (2019) (# citations 521)

Tags: Synthetic biology

screenshot of Chopchop

Chromatic

Publication: (direct link) (doi link) (2018) (# citations 1)

Language: WASM

Tags: Alignment viewer

Platform: Web

screenshot of Chromatic

cnvCurator

Publication: (direct link) (doi link) (2015) (# citations 1)

Language: Java

Tags: CNV, Annotation, Deadlink?

Platform: Desktop

screenshot of cnvCurator

D3GB

Publication: (doi link) (2017) (# citations 6)

Language: JS, D3

Tags: Special-purpose

Platform: Web

screenshot of D3GB

DNASkittle

Publication: (doi link) (2009) (# citations 6)

Tags: Special-purpose

Github Stargazers: 5

Platform: Web

screenshot of DNASkittle

EaSeq

Publication: (direct link) (doi link) (2016) (# citations 153)

Tags: Special-purpose, Epigenomics

Platform: Desktop

screenshot of EaSeq

Ribbon

Publication: (direct link) (doi link) (2020) (# citations 17)

Language: JS

Tags: SV, Alignment viewer

Github Stargazers: 219

Platform: Web

screenshot of Ribbon

GenomeSpy

Language: JS, WebGL

Tags: CNV, GWAS, Linear, MSA

Github Stargazers: 97

Platform: Web

screenshot of GenomeSpy

Genoverse

Language: JS

Tags: General, Linear

Github Stargazers: 89

Platform: Web

screenshot of Genoverse

Gnomad browser

Publication: (doi link) (2020) (# citations 3046)

Language: JS

Tags: Special-purpose, Linear, Population

Github Stargazers: 61

Platform: Web, Silo

screenshot of Gnomad browser

Gremlin

Publication: (doi link) (2010) (# citations 19)

Tags: SV, Linear

Platform: Web

screenshot of Gremlin

Hawkeye

Publication: (direct link) (doi link) (2007) (# citations 54)

Language: C++

Tags: Special-purpose, Alignment viewer, Assembly QC

Platform: Desktop

screenshot of Hawkeye

Human genome dating

Publication: (doi link) (2020) (# citations 57)

Language: JS

Tags: Population, GWAS

Note: made with vega/d3

Platform: Web

screenshot of Human genome dating

Icarus QUAST

Publication: (doi link) (2016) (# citations 69)

Tags: Assembly QC

Github Stargazers: 252

Platform: Web

screenshot of Icarus QUAST

InGAP-SV

Publication: (doi link) (2011) (# citations 59)

Language: Java

Tags: SV, Alignment viewer

Platform: Desktop

screenshot of InGAP-SV

Introgression browser

Publication: (direct link) (doi link) (2015) (# citations 17)

Language: Python

Tags: SV, Introgression

Platform: Web

screenshot of Introgression browser

IslandViewer and IslandPlot

Publication: (doi link) (2015) (# citations 241)

Language: JS, D3

Tags: Special-purpose

Note: web app using it here https://pathogenomics.sfu.ca/islandviewer uses D3, SVG

Github Stargazers: 32

Platform: Web

screenshot of IslandViewer and IslandPlot

Locuszoom

Publication: (doi link) (2010) (# citations 1843)

Tags: GWAS, Population

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

Github Stargazers: 121

Platform: Web

screenshot of Locuszoom

LookSeq

Publication: (doi link) (2009) (# citations 49)

Tags: Alignment viewer

Github Stargazers: 4

Platform: Web

screenshot of LookSeq

Panoptes

Publication: (doi link) (2017) (# citations 5)

Language: Python, JS

Tags: Special-purpose, Population

Github Stargazers: 36

screenshot of Panoptes

MapView

Publication: (direct link) (doi link) (2009) (# citations 64)

Tags: Special-purpose, Alignment viewer

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

Platform: Desktop

screenshot of MapView

NGB

Language: Java

Tags: Special-purpose, Alignment viewer

Github Stargazers: 133

Platform: Web

screenshot of NGB

SEQing

Publication: (doi link) (2020) (# citations 4)

Language: Python

Tags: Special-purpose

Github Stargazers: 6

Platform: Web

screenshot of SEQing

SFARI

Publication: (doi link) (2010) (# citations 161)

Tags: Special-purpose, CNV

Platform: Web, Silo

screenshot of SFARI

SNPitty

Publication: (direct link) (doi link) (2018) (# citations 11)

Language: R

Tags: Special-purpose, CNV

Platform: Web

screenshot of SNPitty

SplitThreader

Publication: (doi link) (2016) (# citations 10)

Language: JS, PHP

Tags: SV, CNV

Github Stargazers: 65

Platform: Web

screenshot of SplitThreader

Staden

Publication: (doi link) (2010) (# citations 167)

Language: C, Tcl/Tk

Tags: Special-purpose, Alignment viewer, Assembly

Platform: Desktop

screenshot of Staden

TASUKE

Publication: (doi link) (2019) (# citations 12)

Tags: Special-purpose, Pangenome

Note: info about multi-genome-browser https://tasuke.dna.affrc.go.jp/

Platform: Web

screenshot of TASUKE

TE-nest

Publication: (doi link) (2007) (# citations 54)

Tags: Special-purpose, Transposons, Deadlink?

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/

Platform: Web, CGI, Server

screenshot of TE-nest

Transposcope

Publication: (doi link) (2020) (# citations 0)

Language: JS

Tags: Special-purpose, Transposons

Github Stargazers: 5

Platform: Web

screenshot of Transposcope

UGENE

Publication: (doi link) (2012) (# citations 1395)

Language: C++

Tags: Special-purpose

Github Stargazers: 150

Platform: Desktop

screenshot of UGENE

Vials

Publication: (doi link) (2016) (# citations 13)

Tags: Special-purpose, Splicing

Github Stargazers: 13

Platform: Web

No screenshot

BasePlayer

Publication: (direct link) (doi link) (2018) (# citations 18)

Language: Java

Tags: General

Github Stargazers: 4

Platform: Desktop

screenshot of BasePlayer

IGB

Publication: (direct link) (doi link) (2016) (# citations 232)

Language: Java

Tags: General, Alignment viewer

Platform: Desktop

screenshot of IGB

IGV

Publication: (doi link) (2011) (# citations 8303)

Language: Java

Tags: General, Alignment viewer, SV, Quantitative

Github Stargazers: 492

Platform: Desktop

screenshot of IGV

Savant

Publication: (direct link) (doi link) (2012) (# citations 42)

Language: Java

Tags: General, SV, Alignment viewer

Github Stargazers: 12

Platform: Desktop

screenshot of Savant

Tablet

Publication: (doi link) (2012) (# citations 634)

Language: Java

Tags: General, Alignment viewer

Github Stargazers: 29

Platform: Desktop

screenshot of Tablet

Biodalliance

Publication: (doi link) (2011) (# citations 87)

Language: JS

Tags: General, Alignment viewer

Github Stargazers: 217

Platform: Web

screenshot of Biodalliance

GBrowse 2

Publication: (doi link) (2013) (# citations 95)

Language: Perl

Tags: General

Note: Original gbrowse paper https://doi.org/10.1101/gr.403602

Github Stargazers: 46

Platform: Web

screenshot of GBrowse 2

GenomeMaps

Publication: (direct link) (doi link) (2013) (# citations 22)

Language: JS

Tags: General, Deadlink

Github Stargazers: 38

screenshot of GenomeMaps

Gosling

Publication: (doi link) (2022) (# citations 1)

Language: JS, WebGL, Typescript, React

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

Github Stargazers: 97

Platform: Web

screenshot of Gosling

HiGlass

Publication: (doi link) (2018) (# citations 252)

Language: JS, WebGL

Tags: General, Epigenomics, Hi-C

Github Stargazers: 242

Platform: Web, Server

screenshot of HiGlass

IGV.js

Publication: (doi link) (2020) (# citations 21)

Language: JS

Tags: General, Alignment viewer

Github Stargazers: 513

Platform: Web

screenshot of IGV.js

JBrowse

Publication: (doi link) (2016) (# citations 453)

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

Github Stargazers: 429

Platform: Web, Desktop

screenshot of JBrowse

JBrowse 2

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

Github Stargazers: 92

Platform: Web

screenshot of JBrowse 2

Kero-BROWSE

Publication: (doi link) (2017) (# citations 32)

Language: JS

Tags: General, SV, Alignment viewer, Comparative

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

Github Stargazers: 6

Platform: Web

screenshot of Kero-BROWSE

Nucleome browser

Publication: (doi link) (2022) (# citations 1)

Language: JS

Tags: General, Multi

Note: github at https://github.com/nucleome

Platform: Web

screenshot of Nucleome browser

Pileup.js

Publication: (doi link) (2016) (# citations 16)

Language: JS

Tags: General, SV

Github Stargazers: 262

Platform: Web

screenshot of Pileup.js

Trackster

Publication: (doi link) (2012) (# citations 21)

Tags: General

Platform: Web

screenshot of Trackster

UCSC genome browser

Publication: (doi link) (2002) (# citations 4263)

Tags: General

Github Stargazers: 167

Platform: Web, Silo

screenshot of UCSC genome browser

WashU epigenomics browser

Publication: (doi link) (2019) (# citations 136)

Language: JS, React

Tags: General, Epigenomics, Hi-C

Note: features redesign, there is also a legacy version

Github Stargazers: 41

Platform: Web

screenshot of WashU epigenomics browser

Zenbu

Publication: (doi link) (2014) (# citations 130)

Tags: General

Platform: Web

screenshot of Zenbu

cgplot

Language: Python

Tags: Static, Dotplot, Comparative

Github Stargazers: 7

screenshot of cgplot

D-GENIES

Publication: (doi link) (2018) (# citations 213)

Language: JS, Python, D3

Tags: Dotplot, Comparative

Github Stargazers: 73

Platform: Web

screenshot of D-GENIES

Delly-maze

Publication: (doi link) (2012) (# citations 1254)

Language: Python

Tags: Dotplot, Static, Comparative

Note: see also https://www.gear-genomics.com/maze/

Github Stargazers: 9

screenshot of Delly-maze

Discoplot

Publication: (doi link) (2015) (# citations 0)

Language: Python

Tags: Dotplot, Static, Comparative

Github Stargazers: 9

screenshot of Discoplot

Dot

Language: JS, Python

Tags: Dotplot, Comparative

Note: Python data preparation script

Github Stargazers: 17

Platform: Web

screenshot of Dot

Dotlet

Publication: (doi link) (2000) (# citations 73)

Language: JS, React

Tags: Dotplot

Note: The original publication was 2000 but updated ~2020 with reactjs

Github Stargazers: 2

Platform: Web

screenshot of Dotlet

iLambda/Dotplot

Tags: Dotplot

Github Stargazers: 1

Platform: Web

No screenshot

dotPlotly

Language: R, Shiny

Tags: Dotplot, Comparative

Github Stargazers: 128

Platform: Web

screenshot of dotPlotly

Dottup

Tags: Dotplot

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

screenshot of Dottup

FlexiDot

Publication: (doi link) (2018) (# citations 36)

Language: Python

Tags: Dotplot

Github Stargazers: 72

Platform: CLI

screenshot of FlexiDot

Gepard

Publication: (doi link) (2007) (# citations 485)

Language: Java

Tags: Dotplot, Comparative

Github Stargazers: 36

Platform: Desktop

screenshot of Gepard

Jdot

Language: JS

Tags: Dotplot, Comparative

Github Stargazers: 1

Platform: Web

screenshot of Jdot

last-dotplot

Language: Python, C++

Tags: Dotplot, Comparative

Platform: CLI, Web-server

screenshot of last-dotplot

mcutils

Language: R, C++

Tags: Dotplot, Static, Comparative

Note: https://twitter.com/mjpchaisson/status/1040363992206569472

Github Stargazers: 12

screenshot of mcutils

Mummer-idotplot

Language: JS, Python

Tags: Dotplot, Comparative

Github Stargazers: 21

Platform: Web, CLI

No screenshot

Mummerplot

Publication: (doi link) (2004) (# citations 3704)

Language: GNUPlot

Tags: Dotplot, Static, Comparative

Github Stargazers: 309

screenshot of Mummerplot

Redotable

Language: Java

Tags: Dotplot, Comparative

Github Stargazers: 8

Platform: Desktop

screenshot of Redotable

Chip Monk

Publication: (doi link) (2007) (# citations 3)

Language: Java

Tags: Epigenomics

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

Platform: Desktop

screenshot of Chip Monk

Chipster

Publication: (doi link) (2011) (# citations 239)

Language: Java

Tags: Epigenomics, CNV

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

Github Stargazers: 34

Platform: Desktop

screenshot of Chipster

cisGenome Browser

Publication: (doi link) (2010) (# citations 32)

Language: C

Tags: Epigenomics

Platform: Desktop

screenshot of cisGenome Browser

Epiviz

Publication: (doi link) (2020) (# citations 1)

Language: JS, R, D3

Tags: Epigenomics

Github Stargazers: 66

Platform: Web

screenshot of Epiviz

HiPiler

Publication: (doi link) (2018) (# citations 27)

Language: JS

Tags: Epigenomics, Hi-C, Higlass integration

Github Stargazers: 11

Platform: Web

screenshot of HiPiler

Juicebox

Publication: (direct link) (doi link) (2016) (# citations 688)

Language: Java

Tags: Epigenomics, Hi-C

Github Stargazers: 167

Platform: Desktop

screenshot of Juicebox

Juicebox.js

Publication: (direct link) (doi link) (2018) (# citations 139)

Language: JS

Tags: Epigenomics, Hi-C

Github Stargazers: 15

Platform: Web

screenshot of Juicebox.js

Peax

Publication: (doi link) (2020) (# citations 7)

Language: JS

Tags: Epigenomics, Higlass integration

Github Stargazers: 61

Platform: Web

screenshot of Peax

eweitz/Ideogram

Language: JS

Tags: Ideogram

Github Stargazers: 228

Platform: Web

screenshot of eweitz/Ideogram

Ideogram

Publication: (doi link)

Language: SVG

Tags: Ideogram, Static

Github Stargazers: 76

screenshot of Ideogram

Ideoplot

Language: R

Tags: Ideogram, Static

Github Stargazers: 12

No screenshot

karyoploteR

Publication: (doi link) (2017) (# citations 299)

Language: R

Tags: Ideogram, Static

Github Stargazers: 232

screenshot of karyoploteR

KaryotypeSVG

Language: JS, SVG

Tags: Ideogram

Github Stargazers: 5

Platform: Web

screenshot of KaryotypeSVG

UCSC Genome Graphs

Publication: (doi link) (2002) (# citations 4263)

Tags: Ideogram

Github Stargazers: 167

Platform: Web, Form, Silo

screenshot of UCSC Genome Graphs

iGenomics

Publication: (doi link) (2020) (# citations 10)

Language: Objective-C

Tags: Mobile, Alignment viewer

Github Stargazers: 33

screenshot of iGenomics

Panacaea

Publication: (doi link) (2018) (# citations 8)

Tags: Pangenome

Github Stargazers: 6

screenshot of Panacaea

Panache

Publication: (doi link) (2021) (# citations 4)

Language: JS, VueJS

Tags: Pangenome

Github Stargazers: 32

screenshot of Panache

Protael

Publication: (direct link) (doi link) (2015) (# citations 8)

Language: JS

Tags: Protein, MSA

Github Stargazers: 18

Platform: Web

screenshot of Protael

ProteinPaint

Publication: (direct link) (doi link) (2015) (# citations 173)

Tags: Protein, Cancer, Lollipops

Note: Not open source

Platform: Web

screenshot of ProteinPaint

GenomePaint

Publication: (direct link) (doi link) (2021) (# citations 9)

Tags: CNV, Linear, Cancer, Lollipops

Note: Not open source

Platform: Web

screenshot of GenomePaint

pViz

Publication: (doi link) (2014) (# citations 18)

Language: JS

Tags: Protein

Github Stargazers: 62

Platform: Web

screenshot of pViz

UCSC Xena

Publication: (doi link) (2020) (# citations 802)

Language: JS

Tags: Heatmap, Population

Github Stargazers: 49

Platform: Web

screenshot of UCSC Xena

Dotter

Publication: (doi link) (1995) (# citations 444)

Tags: Dotplot

Platform: CLI

screenshot of Dotter

LinearDisplay.pl

Publication: (doi link) (2019) (# citations 273)

Language: Perl

Tags: Comparative

Note: readme says to cite this paper

Github Stargazers: 2

Platform: CLI

screenshot of LinearDisplay.pl

Gview

Publication: (doi link) (2010) (# citations 222)

Language: Perl, Java, Java web start

Tags: Circular, Linear, Pangenome, Microbiology

Platform: Web

screenshot of Gview

FastANI

Publication: (doi link) (2018) (# citations 1235)

Language: C++

Tags: Comparative, Microbiology

Github Stargazers: 237

screenshot of FastANI

JGI/IMG

Tags: Dotplot, Linear, Microbiology

Note: Dotplot use MUMmer

Platform: Web, Silo

screenshot of JGI/IMG

clinker

Publication: (direct link) (doi link) (2021) (# citations 123)

Language: JS

Tags: Comparative, Gene order

Github Stargazers: 350

Platform: Web

screenshot of clinker

PopSV

Publication: (doi link) (2018) (# citations 30)

Language: R

Tags: Population, SV

Github Stargazers: 25

Platform: Web

screenshot of PopSV

Shasta

Publication: (doi link) (2020) (# citations 185)

Language: C++

Tags: Graph

Note: Uses graphviz

Platform: Web, Localhost, CLI

screenshot of Shasta

LINX

Publication: (doi link) (2019) (# citations 24)

Language: Java, Circos integration

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

Note: part of the PURPLE/GRIDSS/LINX pipeline

Github Stargazers: 109

screenshot of LINX

PURPLE

Publication: (doi link) (2019) (# citations 24)

Tags: CNV, Cancer

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

Github Stargazers: 109

screenshot of PURPLE

SMRT View

Tags: SV

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

Github Stargazers: 101

screenshot of SMRT View

spinteny

Language: JS

Tags: Exotic, Comparative

Github Stargazers: 1

screenshot of spinteny

bcftools roh

Publication: (doi link) (2016) (# citations 320)

Language: Python, C, Matplotlib

Tags: Static

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

Github Stargazers: 469

screenshot of bcftools roh

mocha

Publication: (doi link) (2018) (# citations 166)

Language: C, WDL, R

Tags: CNV

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

Github Stargazers: 54

screenshot of mocha

ALVIS (MSA viewer)

Publication: (direct link) (doi link) (2016) (# citations 8)

Tags: MSA

Note: Introduces sequence bundles concept, also see web app version https://www.ebi.ac.uk/goldman-srv/sequencebundles/ source code https://bitbucket.org/schwarzlab/alvis/src/master/

screenshot of ALVIS (MSA viewer)

ALVIS (chimeric alignment viewer)

Publication: (direct link) (doi link) (2021) (# citations 5)

Language: Java

Tags: QC, Assembly

Github Stargazers: 14

screenshot of ALVIS (chimeric alignment viewer)

GfaViz

Publication: (direct link) (doi link) (2018) (# citations 11)

Language: C++

Tags: Graph

Github Stargazers: 43

screenshot of GfaViz

Nextclade

Publication: (doi link) (2021) (# citations 103)

Language: JS, React, D3

Tags: Phylogenetics, Microbiology

Note: Related usage on nextstrain app also

screenshot of Nextclade

vcfR

Publication: (doi link) (2016) (# citations 373)

Language: R

Tags: QC, Population, Coverage

Note: image shows chromoqc output

Github Stargazers: 191

screenshot of vcfR

asgart

Publication: (direct link) (doi link) (2018) (# citations 5)

Language: Rust

Tags: SV, Ideogram, Circular, Linear

Github Stargazers: 13

screenshot of asgart

MashMap

Publication: (doi link) (2018) (# citations 67)

Language: Perl, C++

Tags: Dotplot

Github Stargazers: 184

screenshot of MashMap

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

Github Stargazers: 12

screenshot of udon

AnnoJ

Language: JS

Tags: Methylation

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

Platform: Web

screenshot of AnnoJ

methylartist

Publication: (doi link) (2021) (# citations 3)

Language: Python

Tags: Long reads, Methylation

Github Stargazers: 53

screenshot of methylartist

gingko

Publication: (doi link) (2015) (# citations 163)

Language: PHP, JS

Tags: Single cell, CNV

Github Stargazers: 42

Platform: Web

screenshot of gingko

casper

Publication: (direct link) (doi link) (2020) (# citations 43)

Language: R

Tags: Single cell, CNV

Github Stargazers: 58

screenshot of casper

LDBlockShow

Publication: (direct link) (doi link) (2020) (# citations 41)

Language: C++, Perl

Tags: GWAS, Population

Github Stargazers: 75

screenshot of LDBlockShow

clinker (gene fusion software)

Publication: (direct link) (doi link) (2018) (# citations 11)

Language: R

Tags: Gene fusion

Github Stargazers: 43

screenshot of clinker (gene fusion software)

arriba

Publication: (direct link) (doi link) (2021) (# citations 63)

Language: C++, R

Tags: Gene fusion

Github Stargazers: 150

screenshot of arriba

FusionInspector

Publication: (doi link) (2021) (# citations 0)

Language: Perl, JS

Tags: Gene fusion

Note: Uses igv.js

Github Stargazers: 36

screenshot of FusionInspector

NeoLoopFinder

Publication: (doi link) (2021) (# citations 13)

Language: Python

Tags: SV, Hi-C

Github Stargazers: 28

screenshot of NeoLoopFinder

alen

Language: Rust

Tags: MSA, Text based

Github Stargazers: 46

screenshot of alen

Aquaria

Publication: (doi link) (2015) (# citations 50)

Tags: Protein, MSA

Platform: Web

screenshot of Aquaria

vega

Publication: (doi link) (2004) (# citations 89)

Tags: Assembly, Historical, Genetic map

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

Platform: Web

screenshot of vega

nightingale/protvista

Publication: (doi link) (2017) (# citations 42)

Language: JS, Typescript

Tags: Protein, MSA

Note: Used on InterProScan website https://www.ebi.ac.uk/interpro/

Github Stargazers: 80

Platform: Web

screenshot of nightingale/protvista

ArchR

Publication: (doi link) (2021) (# citations 191)

Language: R

Tags: Single cell

Github Stargazers: 235

screenshot of ArchR

PGAP-X

Publication: (direct link) (doi link) (2018) (# citations 17)

Language: C++

Tags: Pangenome

Platform: Desktop

screenshot of PGAP-X

MAVIS

Publication: (doi link) (2018) (# citations 15)

Language: Python

Tags: Gene fusion, SV

Github Stargazers: 60

screenshot of MAVIS

ProViz

Publication: (direct link) (doi link) (2016) (# citations 53)

Language: JS

Tags: MSA, Protein

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

screenshot of ProViz

SVPV

Publication: (direct link) (doi link) (2017) (# citations 7)

Language: Python

Tags: SV, Coverage

Github Stargazers: 28

screenshot of SVPV

pretzel

Publication: (doi link) (2019) (# citations 16)

Language: JS, D3

Tags: Comparative, Genetic map

Github Stargazers: 29

screenshot of pretzel

splicejam

Publication: (doi link) (2019) (# citations 25)

Language: R

Tags: Splicing, Sashimi

Github Stargazers: 20

screenshot of splicejam

Plotgardener

Publication: (doi link) (2022) (# citations 3)

Language: R

Tags: Hi-C, Coverage

Github Stargazers: 191

screenshot of Plotgardener

MIRA

Publication: (doi link) (2004) (# citations 829)

Language: C++

Tags: Assembly, Alignment viewer, Historical

Note: orig paper also describes mira here http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.23.7465&rep=rep1&type=pdf

screenshot of MIRA

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

Github Stargazers: 7

screenshot of oxford-plots

IGGE

Publication: (doi link) (2021) (# citations 2)

Tags: Graph, Exotic

Note: Not open source

Github Stargazers: 1

screenshot of IGGE

PipMaker

Publication: (doi link) (2000) (# citations 849)

Tags: Comparative, Repeat, Annotation

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

screenshot of PipMaker

MEGA-X

Publication: (doi link) (2021) (# citations 618)

Tags: MSA, Phylogenetics

Note: original paper from 1994 but actively updated. requires EULA for download

Platform: Desktop

screenshot of MEGA-X

Haploview

Publication: (doi link) (2004) (# citations 10907)

Language: Java

Tags: Population, LD

Platform: Desktop

screenshot of Haploview

WGDI

Publication: (direct link) (doi link) (2021) (# citations 18)

Language: Python

Tags: Comparative, Dotplot, Circular

Github Stargazers: 46

screenshot of WGDI

AmpliconArchitect

Publication: (doi link) (2019) (# citations 74)

Language: Python

Tags: SV, Cancer

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

Github Stargazers: 87

screenshot of AmpliconArchitect

PGV

Publication: (direct link) (doi link) (2021) (# citations 1)

Language: Python

Tags: Pangenome, Dotplot, Comparative

Github Stargazers: 14

Platform: Web

screenshot of PGV

REViewer

Publication: (direct link) (doi link) (2021) (# citations 1)

Tags: Repeats

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

Github Stargazers: 43

screenshot of REViewer

Trackplot

Publication: (doi link) (2014) (# citations 141)

Language: R

Tags: Coverage, Gene structure

Note: suggests citing bwtool linked here

Github Stargazers: 55

screenshot of Trackplot

gcMapExplorer

Publication: (doi link) (2017) (# citations 18)

Language: Python

Tags: Hi-C

Github Stargazers: 16

screenshot of gcMapExplorer

BRIG

Publication: (direct link) (doi link) (2011) (# citations 1737)

Language: Java

Tags: Comparative, Circular

Github Stargazers: 13

Platform: Desktop

screenshot of BRIG

ggplot2 manhattan plot

Language: R, ggplot2

Tags: GWAS

Note: This is not a preconfigured tool but a blog post tutorial with tidy data and ggplot2

screenshot of ggplot2 manhattan plot

ete

Publication: (doi link) (2016) (# citations 1099)

Language: Python

Tags: MSA, Phylogenetics

Github Stargazers: 632

screenshot of ete

ggtree

Publication: (doi link) (2016) (# citations 1699)

Language: R

Tags: MSA, Phylogenetics, ggplot2

Note: see https://yulab-smu.top/treedata-book/chapter7.html?q=msa#msaplot for MSA example

Github Stargazers: 644

screenshot of ggtree

GeneViTo

Publication: (doi link) (2003) (# citations 7)

Language: Java

Tags: Microbiology, General

Platform: Desktop

screenshot of GeneViTo

CGView

Publication: (doi link) (2008) (# citations 742)

Language: JS

Tags: Circular, Microbiology

Note: See also CGView comparison tool and other related https://paulstothard.github.io/cgview_comparison_tool/

Github Stargazers: 24

Platform: Web

screenshot of CGView

miropeats

Publication: (direct link) (doi link) (1995) (# citations 29)

Language: Perl, C

Tags: Comparative, Repeats, Synteny, Historical

Note: image from 2021 paper https://www.biorxiv.org/content/10.1101/2021.12.08.471837v1.full.pdf

screenshot of miropeats

Slinker

Publication: (direct link) (doi link) (2021) (# citations 1)

Language: Python

Tags: Splicing, Coverage

Note: See also, clinker (gene fusion software)

Github Stargazers: 12

screenshot of Slinker

syntenyPlotteR

Language: R, ggplot2

Tags: Comparative

Github Stargazers: 14

screenshot of syntenyPlotteR

StainedGlass

Publication: (doi link) (2022) (# citations 6)

Language: R, Python, JS

Tags: Repeats, Heatmap, Higlass integration

Github Stargazers: 34

Platform: Web, CLI

screenshot of StainedGlass

SimpleSynteny

Publication: (doi link) (2016) (# citations 70)

Tags: Comparative

Platform: Web, Server

screenshot of SimpleSynteny

Cinteny

Publication: (doi link) (2007) (# citations 90)

Tags: Comparative

Platform: Web, Server

screenshot of Cinteny

DAGchainer

Publication: (doi link) (2004) (# citations 260)

Language: Perl, Java

Tags: Dotplot, Comparative

screenshot of DAGchainer

EvolutionHighway

Language: Java, Applet

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

screenshot of EvolutionHighway

Smash++

Publication: (doi link) (2020) (# citations 7)

Language: C++

Tags: Comparative

Github Stargazers: 47

screenshot of Smash++

plotsr

Publication: (doi link) (2022) (# citations 2)

Language: Python

Tags: Comparative, SV

Note: Blurs the line between synteny and SV visualization, a good thing!

Github Stargazers: 140

screenshot of plotsr

seqvisr

Language: R

Tags: MSA, Protein

Github Stargazers: 3

screenshot of seqvisr

drawProteins

Publication: (doi link) (2018) (# citations 21)

Language: R, ggplot2

Tags: Protein

Github Stargazers: 23

screenshot of drawProteins

IBS (Illustrator for Biological Sequences)

Publication: (doi link) (2015) (# citations 529)

Language: Java

Tags: Protein

Platform: Silo, Web, Desktop

screenshot of IBS (Illustrator for Biological Sequences)

PFAM generate_graphic

Tags: Protein

Note: Also see guide here https://pfam.xfam.org/help#tabview=tab10

Platform: Silo, Web

screenshot of PFAM generate_graphic

SnoopCGH

Publication: (doi link) (2009) (# citations 8)

Language: Java

Tags: CNV, ArrayCGH

screenshot of SnoopCGH

Genovar

Publication: (doi link) (2012) (# citations 2)

Language: Java

Tags: CNV, ArrayCGH, Alignment

screenshot of Genovar

VAMP

Publication: (doi link) (2006) (# citations 90)

Language: Java

Tags: Deadlink, CNV, ArrayCGH

Platform: Applet, Desktop

screenshot of VAMP

CGH-Explorer

Publication: (doi link) (2004) (# citations 111)

Language: Java

Tags: Deadlink, CNV, ArrayCGH

Platform: Desktop

screenshot of CGH-Explorer

GenomeMatcher

Publication: (doi link) (2008) (# citations 186)

Language: Objective-C

Tags: Comparative

Platform: Desktop, Mac

screenshot of GenomeMatcher

DNAVis

Publication: (doi link) (2005) (# citations 6)

Language: C++, OpenGL

Tags: Deadlink, Comparative

Platform: Desktop

screenshot of DNAVis

SynBrowse

Publication: (doi link) (2005) (# citations 52)

Language: Perl

Tags: Comparative, GBrowse integration

Platform: Web

screenshot of SynBrowse

Sybil

Publication: (doi link) (2007) (# citations 52)

Language: Perl

Tags: Comparative, GBrowse integration

Note: Download https://sourceforge.net/projects/sybil/

Platform: Web

screenshot of Sybil

SyntenyPortal

Publication: (doi link) (2016) (# citations 30)

Language: JS

Tags: Comparative, Circular

Platform: Web

screenshot of SyntenyPortal

CHROMEISTER

Publication: (doi link) (2019) (# citations 10)

Language: C, R

Tags: Comparative, Dotplot

Github Stargazers: 23

screenshot of CHROMEISTER

r2cat

Publication: (doi link) (2009) (# citations 100)

Language: Java

Tags: Comparative, Dotplot

Github Stargazers: 2

screenshot of r2cat

Seaview

Publication: (doi link) (2009) (# citations 4025)

Language: C++

Tags: MSA, Phylogenetics

Platform: Desktop

screenshot of Seaview

SequenceServer

Publication: (doi link) (2019) (# citations 77)

Language: Ruby, JS

Tags: BLAST, Comparative, Circular

Github Stargazers: 238

Platform: Web

screenshot of SequenceServer

numbat

Publication: (doi link) (2022) (# citations 0)

Language: R

Tags: Single cell, CNV

Github Stargazers: 48

screenshot of numbat

ggtranscript

Publication: (doi link) (2022) (# citations 0)

Language: R

Tags: Gene structure

Github Stargazers: 62

screenshot of ggtranscript

CIAlign

Publication: (doi link) (2022) (# citations 5)

Language: Python

Tags: MSA

Note: Has useful utility functions to clean gaps and trim MSAs

Github Stargazers: 68

screenshot of CIAlign

CoolBox

Publication: (doi link) (2021) (# citations 3)

Language: Python

Tags: Epigenomics, Hi-C

Note: fork of pyGenomeTracks

Github Stargazers: 170

Platform: CLI, Web

screenshot of CoolBox

GECO

Publication: (doi link) (2006) (# citations 21)

Language: Java

Tags: Microbiology, Compararive

Platform: Web, Deadlink, No binary or source available

screenshot of GECO

Orchestral

Publication: (doi link) (2013) (# citations 4)

Language: C++, OpenGL

Tags: CNV, Large display, No binary or source available

screenshot of Orchestral

PSAT

Publication: (doi link) (2008) (# citations 25)

Tags: Comparative, Deadlink, No binary or source available

Platform: Web, Silo

screenshot of PSAT

UTGB (University of Tokyo Genome Browser)

Publication: (doi link) (2009) (# citations 11)

Language: Java

Tags: General

Github Stargazers: 2

Platform: Web, Servlet

screenshot of UTGB (University of Tokyo Genome Browser)

Combo

Publication: (doi link) (2006) (# citations 37)

Language: Java

Tags: Comparative

Note: Based on the tool 'Argo'

screenshot of Combo

CNSpector

Publication: (doi link) (2019) (# citations 11)

Language: R, Shiny

Tags: CNV

Github Stargazers: 5

screenshot of CNSpector

GenomeSyn

Language: Perl

Tags: Comparative, Ideogram, Deadlink

Github Stargazers: 6

Platform: Web, Desktop

screenshot of GenomeSyn

CMPlot

Publication: (doi link) (2021) (# citations 100)

Language: R

Tags: GWAS

Github Stargazers: 317

screenshot of CMPlot

PhenoGram

Publication: (doi link) (2013) (# citations 125)

Language: Ruby

Tags: Ideogram

Note: Can be web server or download

Platform: Web, Silo, CLI

screenshot of PhenoGram

RIdeogram

Publication: (doi link) (2020) (# citations 93)

Language: R

Tags: Ideogram, Comparative

Github Stargazers: 113

screenshot of RIdeogram

modbamtools

Publication: (doi link) (2022) (# citations 0)

Language: Python

Tags: Methylation, Epigenomics

Github Stargazers: 18

screenshot of modbamtools

sequenza

Publication: (doi link) (2015) (# citations 386)

Language: R

Tags: CNV

Note: also see https://sequenzatools.bitbucket.io/#/home

screenshot of sequenza

pyCircos

Language: Python

Tags: Circular

Note: See also https://github.com/ponnhide/plasmidviewer

Github Stargazers: 140

screenshot of pyCircos

GeneticsMakie.jl

Publication: (doi link) (2022) (# citations 0)

Language: Julia

Tags: GWAS, Gene structure, LD

Github Stargazers: 38

screenshot of GeneticsMakie.jl

MOSAIC

Publication: (doi link) (2019) (# citations 25)

Language: R

Tags: Local ancestry

screenshot of MOSAIC

Prosite/MyDomains

Publication: (doi link) (2007) (# citations 324)

Tags: Protein

Platform: Web, Silo

screenshot of Prosite/MyDomains

snpit

Language: Python

Tags: Variation, Population

Github Stargazers: 66

screenshot of snpit

local-rearrangements

Language: Python

Tags: Dotplot, SV

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

Github Stargazers: 5

screenshot of local-rearrangements

GeCoViz

Publication: (doi link) (2022) (# citations 0)

Tags: Microbiology, Comparative

Platform: Web, Silo

screenshot of GeCoViz

GGisy

Language: Python, R

Tags: Comparative, Circular

Github Stargazers: 11

screenshot of GGisy

ggmsa

Publication: (doi link) (2022) (# citations 0)

Language: R

Tags: MSA

Note: See also ggtree

Github Stargazers: 139

screenshot of ggmsa

CView

Publication: (doi link) (2022) (# citations 0)

Language: Java

Tags: MSA

screenshot of CView

bigly

Language: Go, Python

Tags: SV, Coverage

Github Stargazers: 37

screenshot of bigly

signac

Publication: (doi link) (2021) (# citations 84)

Language: R

Tags: Coverage, Single cell

Github Stargazers: 177

screenshot of signac

pyGenomeViz

Language: Python

Tags: Comparative

Note: See also https://github.com/moshi4/MGCplotter https://github.com/moshi4/GBKviz https://github.com/moshi4/plot_genome_align_fig

Github Stargazers: 18

screenshot of pyGenomeViz

SODA

Publication: (doi link)

Language: JS, Typescript

Tags: Repeats, Circular, Linear

Note: Describes itself as a low-level library to create larger applications with

Github Stargazers: 2

screenshot of SODA

ShinySyn

Publication: (doi link) (2022) (# citations 0)

Language: R, Shiny

Tags: Comparative

screenshot of ShinySyn

JBR

Language: Java

Tags: Epigenomics

Note: Not open source, at least not on github

Github Stargazers: 5

screenshot of JBR

clonifier

Language: Rust, Typescript, React

Tags: Microbiology, Synthetic biology

Github Stargazers: 1

screenshot of clonifier

ctag

Language: Java, Scala

Tags: Graph, Population

Note: See also hygene https://github.com/ProgrammingLife2017/hygene

screenshot of ctag

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