# List of phylogenetic tree visualization software

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 | CeCILL |
| 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 trees | |
| IcyTree | Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks | |
| Iroki | Automatic 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 interface | |
| Microreact | Link, 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 Online | Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees | |
| PhyloWidget | view, edit, and publish phylogenetic trees online; interfaces with databases | |
| PRESTO | a 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 | OS$^1$ |
| ARB | An integrated software environment for tree visualisation and annotation | LM |
| Archaeopteryx | Java tree viewer and editor (used to be ATV) | |
| BioNumerics | Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data | W |
| Dendroscope | An interactive viewer for large phylogenetic trees and networks | All |
| DensiTree | A viewer capable of viewing multiple overlaid trees. | All |
| FigTree | Simple Java tree viewer able to read newick and nexus tree files. Can be used to color branches and produce vector artwork. | All |
| 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 information | All |
| Treevolution | Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering and pruning | All |
| TreeGraph 2 | Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses | All |
| TreeView | Treeviewing software | All |
| UGENE | An opensource visual interface for Phylip 3.6 package | All |
| TreeViewer | Flexible, modular software to visualise and manipulate phylogenetic trees | All |
$^1$ "All" refers to Microsoft Windows, Apple OSX and Linux; L=Linux, M=Apple Mac, W=Microsoft Windows

## Libraries

| Name | Language | Description |
| Bio.Phylo | Python | Phylo: Part of Biopython, this module provides classes, functions and I/O support for working with phylogenetic trees |
| Bio::Phylo | Perl | A collection of Perl modules for manipulating and visualizing phylogenetic data. Bio::Phylo is one part of a comprehensive suite of Perl biology tools |
| CGRphylo | R | Pipeline based on CGR method for accurate classification and tracking of rapidly evolving viruses |
| ETE | Python | ETE (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 supported |
| GraPhlAn | Python | GraPhlAn 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 trees |
| PhyD3 | Javascript | interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js |
| 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 |
| PhyloPlots.jl | Julia | PhyloPlots.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 |