This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualizing phylogenetic trees.
Online software
Name Description License Annotations QUick Analysis for PhylOgeNY (Aquapony)Javascript tree viewer for Beast 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) EvolView an online tool for visualizing, annotating and managing phylogenetic treesIcyTreeClient-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networksIrokiAutomatic customization and visualization of phylogenetic trees iTOL - interactive Tree Of Life annotate trees with various types of data and export to various graphical formats; scriptable through a batch interfaceMicroreactLink, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines OneZoom uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail Lifemap Fractal-like representation to provide an interactive explorer of the tree of life "à la google maps" Phylo.io View and compare up to 2 trees side by side with interactive HTML5 visualisations 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.PHYLOViZ OnlineWeb-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees PhyloWidget view, edit, and publish phylogenetic trees online; interfaces with databases PRESTOa Phylogenetic tReE viSualisaTion. 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. T-REX (Webserver) Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization TidyTree A client-side HTML5/SVG Phylogenetic Tree Renderer, based on D3.js TreeVector scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java
Desktop software
Name Description OS1Citation ARB An integrated software environment for tree visualisation and annotationLM Archaeopteryx Java tree viewer and editor (used to be ATV)All BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data WBioNumerics protocols used by Pulsenet Dendroscope An interactive viewer for large phylogenetic trees and networks AllDensiTreeA viewer capable of viewing multiple overlaid trees. AllFigTreeSimple Java tree viewer able to read newick and nexus tree files. Can be used to color branches and produce vector artwork. AllRambaut A. 2018. FigTree 1.4.4 github.com accessed 17 April 2018 JEvTrace A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny-inspired analysis.All MEGA Software for statistical analysis of molecular evolution. It includes different tree visualization features All MultiDendrograms Interactive open-source application to calculate and plot phylogenetic trees All PHYLOViZ Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees All SplitsTree Software for viewing trees, cladograms, NeighborNets, and other graphs All TreeDyn Open-source software for tree manipulation and annotation allowing incorporation of meta informationAll Treevolution Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering and pruningAll TreeGraph 2 Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analysesAll TreeView Treeviewing softwareAll UGENE An opensource visual interface for Phylip 3.6 packageAll TreeViewer Flexible, modular software to visualise and manipulate phylogenetic trees All
1 "All" refers to Microsoft Windows, Apple macOS and Linux; L=Linux, M=Apple macOS, W=Microsoft Windows
Libraries Name Language Description CitationBio.PhyloPythonPhylo: Part of Biopython, this module provides classes, functions and I/O support for working with phylogenetic treesBio::PhyloPerlA collection of Perl modules for manipulating and visualizing phylogenetic data. Bio::Phylo is one part of a comprehensive suite of Perl biology toolsCGRphyloRPipeline based on CGR method for accurate classification and tracking of rapidly evolving virusesETEPythonETE (Environment for Tree Exploration) is a toolkit that assists in the automated manipulation, analysis and visualization of trees. ggtree R An R package for tree visualization and annotation with grammar of graphics supportedGraPhlAnPythonGraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. jsPhyloSVG Javascript open-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for Elsevier's interactive treesinteractive-phylogenetic-treeswww.elsevier.com mdendro R Library for the calculation and rendering of agglomerative hierarchical clustering dendrograms and multifurcating neighbor-joining phylogenetic trees PhyD3 Javascript interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js phylotree.js Javascriptphylotree.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 PhyloPlots.jl JuliaPhyloPlots.jl is a julia package for plotting phylogenetic trees and networks, integrated with PhyloNetworks.jl Phytools R Phylogenetic Tools for Comparative Biology (and Other Things) based in R toytree Python Toytree: A minimalist tree visualization and manipulation library for Python
See also
List of phylogenetics software Phylogenetics
References
External links
A 'comprehensive list' of Tree Editors List of Tree Editors