List of phylogenetic tree visualization software#Online software

! Name !! Description

|Javascript tree viewer for Beast

|{{yes|CeCILL}}

| an online tool for phylogenetic tree view (newick format) that allows multiple sequence alignments to be shown together with the trees (fasta format)

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| an online tool for visualizing, annotating and managing phylogenetic trees

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|Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks

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|Automatic customization and visualization of phylogenetic trees

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| annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface

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|Link, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines

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| uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail

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| Fractal-like representation to provide an interactive explorer of the tree of life "à la google maps"

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| View and compare up to 2 trees side by side with interactive HTML5 visualisations

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| 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.

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|Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees

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| view, edit, and publish phylogenetic trees online; interfaces with databases

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|a Phylogenetic tReE viSualisaTion.

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| 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.

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| Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization

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| A client-side HTML5/SVG Phylogenetic Tree Renderer, based on D3.js

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| scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java

! Name

! Description

| An integrated software environment for tree visualisation and annotation

| Java tree viewer and editor (used to be ATV)

| Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data

| An interactive viewer for large phylogenetic trees and networks

|A viewer capable of viewing multiple overlaid trees.

|All

|{{cite bioRxiv|title = DensiTree 2: Seeing Trees Through the Forest|biorxiv = 10.1101/012401|date = 2014-12-08| vauthors = Bouckaert R, Heled J }}

|Simple Java tree viewer able to read newick and nexus tree files. Can be used to color branches and produce vector artwork.

|All

|Rambaut A. 2018. [https://github.com/rambaut/figtree/releases FigTree 1.4.4] github.com accessed 17 April 2018

| A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace{{cite journal | vauthors = Lichtarge O, Bourne HR, Cohen FE | title = An evolutionary trace method defines binding surfaces common to protein families | journal = Journal of Molecular Biology | volume = 257 | issue = 2 | pages = 342–358 | date = March 1996 | pmid = 8609628 | doi = 10.1006/jmbi.1996.0167 }} and other phylogeny-inspired analysis.

| Software for statistical analysis of molecular evolution. It includes different tree visualization features

| All

|{{cite journal | vauthors = Kumar S, Stecher G, Li M, Knyaz C, Tamura K | title = MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms | journal = Molecular Biology and Evolution | volume = 35 | issue = 6 | pages = 1547–1549 | date = June 2018 | pmid = 29722887 | pmc = 5967553 | doi = 10.1093/molbev/msy096 }}

| Interactive open-source application to calculate and plot phylogenetic trees

| Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees

| Software for viewing trees, cladograms, NeighborNets, and other graphs

| All

| {{cite journal | vauthors = Huson DH, Bryant D | title = Application of phylogenetic networks in evolutionary studies | journal = Molecular Biology and Evolution | volume = 23 | issue = 2 | pages = 254–267 | date = February 2006 | pmid = 16221896 | doi = 10.1093/molbev/msj030 | doi-access = free }}

| Open-source software for tree manipulation and annotation allowing incorporation of meta information

| Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering and pruning

| Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses

| Treeviewing software

| An opensource visual interface for Phylip 3.6 package

| Flexible, modular software to visualise and manipulate phylogenetic trees

! Name

! Language

|Python

|[https://biopython.org/wiki/Phylo Phylo]: Part of Biopython, this module provides classes, functions and I/O support for working with phylogenetic trees

|{{Cite journal |last1=Cock |first1=Peter J. A. |last2=Antao |first2=Tiago |last3=Chang |first3=Jeffrey T. |last4=Chapman |first4=Brad A. |last5=Cox |first5=Cymon J. |last6=Dalke |first6=Andrew |last7=Friedberg |first7=Iddo |last8=Hamelryck |first8=Thomas |last9=Kauff |first9=Frank |last10=Wilczynski |first10=Bartek |last11=de Hoon |first11=Michiel J. L. |date=2009-06-01 |title=Biopython: freely available Python tools for computational molecular biology and bioinformatics |url=https://academic.oup.com/bioinformatics/article/25/11/1422/330687 |journal=Bioinformatics |language=en |volume=25 |issue=11 |pages=1422–1423 |doi=10.1093/bioinformatics/btp163 |issn=1367-4811 |pmc=2682512 |pmid=19304878}}

|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

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|R

|Pipeline based on CGR method for accurate classification and tracking of rapidly evolving viruses

|{{Cite journal |last1=Thind |first1=Amarinder Singh |last2=Sinha |first2=Somdatta |date=May 2023 |title=Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants |url=https://www.eurekaselect.com/222599/article |journal=Current Genomics |language=en |volume=24 |issue=3 |pages=187–195 |doi=10.2174/0113892029264990231013112156|pmid=38178984 |pmc=10761335 |s2cid=264500732 }}

|Python

|ETE (Environment for Tree Exploration) is a toolkit that assists in the automated manipulation, analysis and visualization of trees.

|{{Cite journal |last1=Huerta-Cepas |first1=Jaime |last2=Serra |first2=François |last3=Bork |first3=Peer |date=June 2016 |title=ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data |url=https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msw046 |journal=Molecular Biology and Evolution |language=en |volume=33 |issue=6 |pages=1635–1638 |doi=10.1093/molbev/msw046 |issn=0737-4038 |pmc=4868116 |pmid=26921390}}

| R

| An R package for tree visualization and annotation with grammar of graphics supported

|{{cite journal | doi = 10.1111/2041-210X.12628 | vauthors = Yu G, Smith DK, Zhu H, Guan Y, Lam TT | title = ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data | journal = Methods in Ecology and Evolution | volume = 8 | issue = 1 | pages = 28–36 | date = January 1, 2017 | s2cid = 63705866 | doi-access = free | bibcode = 2017MEcEv...8...28Y }}

|Python

|[https://github.com/biobakery/graphlan/wiki GraPhlAn] is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.

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| Javascript

| open-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for Elsevier's interactive trees

|[https://www.elsevier.com/authors/author-services/enrichments/interactive-phylogenetic-trees interactive-phylogenetic-trees]www.elsevier.com {{Webarchive|url=https://web.archive.org/web/20170531175323/https://www.elsevier.com/authors/author-services/enrichments/interactive-phylogenetic-trees |date=2017-05-31 }}{{cite journal | vauthors = Smits SA, Ouverney CC | title = jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web | journal = PLOS ONE | volume = 5 | issue = 8 | pages = e12267 | date = August 2010 | pmid = 20805892 | pmc = 2923619 | doi = 10.1371/journal.pone.0012267 | veditors = Poon AF | bibcode = 2010PLoSO...512267S | doi-access = free }}

| Javascript

| interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js

|{{cite journal | vauthors = Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M | title = PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization | journal = Bioinformatics | volume = 33 | issue = 18 | pages = 2946–2947 | date = September 2017 | pmid = 28525531 | doi = 10.1093/bioinformatics/btx324 | doi-access = free }}

| 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

|{{cite journal | vauthors = Shank SD, Weaver S, Kosakovsky Pond SL | title = phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics | language = En | journal = BMC Bioinformatics | volume = 19 | issue = 1 | pages = 276 | date = July 2018 | pmid = 30045713 | pmc = 6060545 | doi = 10.1186/s12859-018-2283-2 | doi-access = free }}

| Julia

|[https://github.com/cecileane/PhyloPlots.jl PhyloPlots.jl] is a julia package for plotting phylogenetic trees and networks, integrated with [https://github.com/crsl4/PhyloNetworks.jl PhyloNetworks.jl]

|{{cite journal | vauthors = Solís-Lemus C, Bastide P, Ané C | title = PhyloNetworks: A Package for phylogenetic networks | language = En | journal = Molecular Biology and Evolution | volume = 34 | issue = 12 | pages = 3292–3298 | date = 2017| doi = 10.1093/molbev/msx235 | pmid = 28961984 | url = https://academic.oup.com/mbe/article/34/12/3292/4103410 }}

| R

| Phylogenetic Tools for Comparative Biology (and Other Things) based in R

| {{cite journal |author=Revell, LJ |title=phytools: An R package for phylogenetic comparative biology (and other things)|journal=Methods Ecol. Evol. |volume=3 |issue=2|pages=217–223 |year=2012 |doi=10.1111/j.2041-210X.2011.00169.x|s2cid=32670711|doi-access=free|bibcode=2012MEcEv...3..217R }}

| Python

| Toytree: A minimalist tree visualization and manipulation library for Python

| {{cite journal |author=Eaton, DAR | title=Toytree: A minimalist tree visualization and manipulation library for Python| journal=Methods Ecol. Evol. | volume=11| issue=1| pages=187–191 | year=2019| doi=10.1111/2041-210X.13313 | doi-access=free}}