List of phylogenetic tree visualization software

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

Online software[edit]

Name Description Citation
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] 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]
PRESTO a Phylogenetic tReE viSualisaTion. [13]
Taxonium web-based tool for exploration of very large trees including those with millions of nodes, with search and metadata coloring. When provided with a mutation-annotated tree, it illustrates mutations on the tree and displays final genotypes. [14]
T-REX (Webserver) Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization [15]
TidyTree A client-side HTML5/SVG Phylogenetic Tree Renderer, based on D3.js [16]
TreeVector scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java [17]

Desktop software[edit]

Name Description OS1 Citation
ARB An integrated software environment for tree visualisation and annotation LM [18]
Archaeopteryx Java tree viewer and editor (used to be ATV) [19]
BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data W [20]
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 tools All [21]
Dendroscope An interactive viewer for large phylogenetic trees and networks All [22]
DensiTree A viewer capable of viewing multiple overlaid trees. All [23]
FigTree Simple Java tree viewer able to read newick and nexus tree files. Can be used to color branches and produce vector artwork. All [24]
JEvTrace A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace[25] and other phylogeny-inspired analysis. All [26]
MEGA Software for statistical analysis of molecular evolution. It includes different tree visualization features All [27]
MultiDendrograms Interactive open-source application to calculate and plot phylogenetic trees All [28]
PHYLOViZ Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees All [29]
SplitsTree Software for viewing trees, cladograms, NeighborNets, and other graphs All [30]
TreeDyn Open-source software for tree manipulation and annotation allowing incorporation of meta information All [31]
Treevolution Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering and pruning All [32]
TreeGraph 2 Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses All [33]
TreeView Treeviewing software All [34][35]
UGENE An opensource visual interface for Phylip 3.6 package All [36]

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


Name Language Description Citation
ggtree R An R package for tree visualization and annotation with grammar of graphics supported [37]
jsPhyloSVG Javascript open-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for Elsevier's interactive trees [38][39]
PhyD3 Javascript interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js [40]
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 [41]
PhyloPlots.jl Julia PhyloPlots.jl is a julia package for plotting phylogenetic trees and networks, integrated with PhyloNetworks.jl [42]
Phytools R Phylogenetic Tools for Comparative Biology (and Other Things) based in R [43]
toytree Python Toytree: A minimalist tree visualization and manipulation library for Python [44]

See also[edit]


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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 S, Abudahab K, Goater RJ, Fedosejev A, Bhai J, Glasner C, et al. (November 2016). "Microreact: visualizing and sharing data for genomic epidemiology and phylogeography". Microbial Genomics. 2 (11): e000093. doi:10.1099/mgen.0.000093. PMC 5320705. PMID 28348833.
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  9. ^ Robinson O, Dylus D, Dessimoz C (August 2016). " Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web". Molecular Biology and Evolution. 33 (8): 2163–6. arXiv:1602.04258. Bibcode:2016arXiv160204258R. doi:10.1093/molbev/msw080. PMC 4948708. PMID 27189561.
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External links[edit]