List of phylogenetic tree visualization software

This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualising phylogenetic trees.

Online software
Name DescriptionCitation
Aquapony Javascript tree viewer for Beast [1]
ETE toolkit Tree Viewer an online tool for phylogenetic tree view (newick format) that allows multiple sequence alignments to be shown together with the trees (fasta format) [2]
EvolView an online tool for visualizing, annotating and managing phylogenetic trees [3]
IcyTree Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks [4]
Iroki Automatic customization and visualization of phylogenetic trees [5]
iTOL - interactive Tree Of Life annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface [6]
Microreact Link, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines [7]
OneZoom uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail [8]
Phylo.io View and compare up to 2 trees side by side with interactive HTML5 visualisations [9]
PhyloExplorer a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. [10]
PHYLOViZ Online Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees [11]
PhyloWidget view, edit, and publish phylogenetic trees online; interfaces with databases [12]
T-REX (Webserver) Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization [13]
TidyTree A client-side HTML5/SVG Phylogenetic Tree Renderer, based on D3.js [14]
TreeVector scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java [15]

Desktop software
Name DescriptionOS1Citation
ARB An integrated software environment for tree visualisation and annotationLM[16]
Archaeopteryx Java tree viewer and editor (used to be ATV) [17]
BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence dataW
Bio::Phylo A collection of Perl modules for manipulating and visualizing phylogenetic data. Bio::Philo is one part of a comprehensive suite of Perl biology toolsAll[18]
Dendroscope An interactive viewer for large phylogenetic trees and networksAll[19]
DensiTree A viewer capable of viewing multiple overlaid trees. All [20]
JEvTrace A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace[21] and other phylogeny-inspired analysis.All[22]
MEGA Software for statistical analysis of molecular evolution. It includes different tree visualization features All [23]
MultiDendrograms Interactive open-source application to calculate and plot phylogenetic treesAll[24]
PHYLOViZ Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning TreesAll[25]
TreeDyn Open-source software for tree manipulation and annotation allowing incorporation of meta informationAll[26]
Treevolution Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering and pruningAll[27]
TreeGraph 2 Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analysesAll[28]
TreeView Treeviewing softwareAll[29][30]
UGENE An opensource visual interface for Phylip 3.6 packageAll

1 "All" refers to Microsoft Windows, Apple OSX and Linux; L=Linux, M=Apple Mac, W=Microsoft Windows

Libraries
Name LanguageDescriptionCitation
ggtree R An R package for tree visualization and annotation with grammar of graphics supported [31]
jsPhyloSVG Javascript open-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for Elsevier's interactive trees [32][33]
PhyD3 Javascript interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js [34]
phylotree.js Javascript phylotree.js is a library that extends the popular data visualization framework D3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees [35]
Phytools R Phylogenetic Tools for Comparative Biology (and Other Things) based in R [36]
toytree Python Toytree: A minimalist tree visualization and manipulation library for Python [37]

See also

References
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  2. Huerta-Cepas J, Dopazo J, Gabaldón T (January 2010). "ETE: a python Environment for Tree Exploration". BMC Bioinformatics. 11: 24. doi:10.1186/1471-2105-11-24. PMC 2820433. PMID 20070885.
  3. Zhang H, Gao S, Lercher MJ, Hu S, Chen WH (July 2012). "EvolView, an online tool for visualizing, annotating and managing phylogenetic trees". Nucleic Acids Research. 40 (Web Server issue): W569–72. doi:10.1093/nar/gks576. PMC 3394307. PMID 22695796.
  4. Vaughan TG (August 2017). "IcyTree: rapid browser-based visualization for phylogenetic trees and networks". Bioinformatics. 33 (15): 2392–2394. doi:10.1093/bioinformatics/btx155. PMC 5860111. PMID 28407035.
  5. Moore RM, Harrison AO, McAllister SM, Polson SW, Wommack KE (February 2020). "Iroki: automatic customization and visualization of phylogenetic trees". PeerJ. 8 (e8584): e8584. doi:10.7717/peerj.8584. PMC 7049256. PMID 32149022.
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  7. Argimón, Silvia; Abudahab, Khalil; Goater, Richard J. E.; Fedosejev, Artemij; Bhai, Jyothish; Glasner, Corinna; Feil, Edward J.; Holden, Matthew T. G.; Yeats, Corin A. (2016-11-30). "Microreact: visualizing and sharing data for genomic epidemiology and phylogeography". Microbial Genomics. 2 (11): e000093. doi:10.1099/mgen.0.000093. ISSN 2057-5858. PMC 5320705. PMID 28348833.
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  11. Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA (July 2016). "PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees". Nucleic Acids Research. 44 (W1): W246–51. doi:10.1093/nar/gkw359. PMC 4987911. PMID 27131357.
  12. Jordan GE, Piel WH (July 2008). "PhyloWidget: web-based visualizations for the tree of life". Bioinformatics. 24 (14): 1641–2. doi:10.1093/bioinformatics/btn235. PMID 18487241.
  13. Boc A, Diallo AB, Makarenkov V (July 2012). "T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks". Nucleic Acids Research. 40 (Web Server issue): W573–9. doi:10.1093/nar/gks485. PMC 3394261. PMID 22675075.
  14. Boyles, Anthony (2019). "TidyTree: Uncompromisingly Flexible Phylogenetic Trees". CDC.
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