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 Description Site Citation
Aquapony Javascript tree viewer for Beast.
Archaeopteryx Java tree viewer and editor (used to be ATV) [1]
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. [2]
ETE toolkit A Python Environment for Tree Exploration (online treeview) [3]
Hypergeny visualise large phylogenies with this hyperbolic tree browser
InfoViz Tree Tools the generic Javascript InfoViz toolkit supports hyperbolic, space and icicle trees
iTOL - interactive Tree Of Life annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface [4]
TreeVector scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java. [5]
jsPhyloSVG open-source javascript library for rendering highly-extensible, customizable phylogenetic trees. [6]
JStree open-source javascript library for viewing and editing phylogenetic trees with HTML5 canvas
OneZoom uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail [7]
Phylodendron different tree styles, branch styles and output graphical formats
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. [8]
Phylo.io View and compare up to 2 trees side by side with interactive HTML5 visualisations [9]
Phyloviewer web-based integrated environment for phylogenomic analysis based on the Bioinformatics Portal System
PhyloWidget view, edit, and publish phylogenetic trees online; interfaces with databases [10]
TRED a tool to visualize and edit phylogenetic trees. Combines a browser-based Javascript client with a Python (web2py) server. Trees are rendered in SVG using Raphael.
Treedraw HTML5 canvas based phylogenetic tree viewer
TreeViz Java tree viewer that does treemaps as well
T-REX (Webserver) Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization [11]
TreeLink Phylogenetic visualization, clustering and data integration. [12]
Microreact Link, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines.
PHYLOViZ Online Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees [13]

Desktop Software

Name Description OS1SiteCitation
ARB An integrated software environment for tree visualisation and annotation.LM[14]
BayesTrees A program designed to display, analyse and manipulate samples of trees, in particular Bayesian samples. W
BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data. W
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 [15]
Dendroscope An interactive viewer for large phylogenetic trees and networks All[16]
DensiTree A viewer capable of viewing multiple overlaid trees. All [17]
ETE A Python toolkit that assists in the visualization of custom phylogenetic tree images (exports as PNG, PDF and SVG). All [3]
FigTree Modern treeviewer with coloring and collapsingAll
Geneious Pro All-in-one sequence analysis, phylogenetics and molecular cloning application with modern treeviewerAll
JEvTrace A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis.All[18]
MultiDendrograms Application to calculate and plot phylogenetic trees All[19]
NJplot Interactive tree plotter, re-roots, exports as PDF All
TreeDyn Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta informationAll[20]
TreeGraph 2 Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analysesAll[21]
TreeView Classic treeviewing software that is very highly cited All[22]
UGENE An opensource visual interface for Phylip 3.6 packageAll
VectorFriends An integrated sequence analysis software with viewer for phylogenetic treesW
PHYLOViZ Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees All[23]

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

See also

References

  1. ↑ Zmasek, CM & Eddy, SR (2001). "TV: display and manipulation of annotated phylogenetic trees". Bioinformatics. 17 (4): 383–384. doi:10.1093/bioinformatics/17.4.383. PMID 11301314.
  2. ↑ Huangkai Zhang; Shenghan Gao; Martin J. Lercher; Songnian Hu & Wei-Hua Chen (Jul 2012). "EvolView, an online tool for visualizing, annotating and managing phylogenetic trees". Nucleic Acids Research. 40 (W1): W569–W572. doi:10.1093/nar/gks576. PMID 22695796.
  3. 1 2 Huerta-Cepas, Jaime; Dopazo, Joaquin; Gabaldon, Toni (2010). "ETE: a python Environment for Tree Exploration". BMC Bioinformatics. 11: 24. doi:10.1186/1471-2105-11-24. PMC 2820433Freely accessible. PMID 20070885.
  4. ↑ Letunic, Ivica; Bork, Peer (January 1, 2007). "Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation" (PDF). Bioinformatics. Cambridge: Oxford University Press. 23 (1): 127–128. doi:10.1093/bioinformatics/btl529. ISSN 1367-4803. PMID 17050570. Retrieved 2015-07-21.
  5. ↑ Pethica, R. and Barker, G. and Kovacs, T. and Gough, J. (2010). "TreeVector: scalable, interactive, phylogenetic trees for the web". PLoS ONE. 5: e8934. doi:10.1371/journal.pone.0008934.
  6. ↑ Smits, SA and Ouverney, CC (2010). Poon, Art F. Y., ed. "jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web". PLoS ONE. 5 (8): e12267. doi:10.1371/journal.pone.0012267. PMC 2923619Freely accessible. PMID 20805892.
  7. ↑ Rosindell, J & Harmon, LJ (2012). "OneZoom: A Fractal Explorer for the Tree of Life". PLoS Biology. 10. doi:10.1371/journal.pbio.1001406.
  8. ↑ Ranwez, V et al., WH (2009). "PhyloExplorer: a web server to validate, explore and query phylogenetic trees". BMC Evolutionary Biology. 9. 9: 108. doi:10.1186/1471-2148-9-108.
  9. ↑ Robinson, Oscar; Dylus, David (2016). "Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web". Molecular Biology and Evolution. doi:10.1093/molbev/msw080. Retrieved 21 April 2016.
  10. ↑ Jordan, EG & Piel, WH (2008). "PhyloWidget: web-based visualizations for the tree of life". Bioinformatics. 24 (14): 1641–1642. doi:10.1093/bioinformatics/btn235. PMID 18487241.
  11. ↑ Boc A, Diallo Alpha B, Makarenkov V (2012). "T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks". Nucleic Acids Research. 40 (W1) (Web Server issue): W573–W579. doi:10.1093/nar/gks485. PMC 3394261Freely accessible. PMID 22675075.
  12. ↑ Allende, Christian; Sohn, Erik; Little, Cedric (2015-12-29). "Treelink: data integration, clustering and visualization of phylogenetic trees". BMC Bioinformatics. 16 (1). doi:10.1186/s12859-015-0860-1. PMC 4696249Freely accessible. PMID 26714661.
  13. ↑ Ribeiro-Gonçalves, Bruno; P. Francisco, Alexandre; Vaz, Cátia; Ramirez, Mário; André Carriço, João (2016-04-21). "PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees". Nucleic Acids Research. 16 (1). doi:10.1093/nar/gkw359. PMID 27131357.
  14. ↑ Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004). "ARB: a software environment for sequence data". Nucleic Acids Res. 32 (4): 1363–71. doi:10.1093/nar/gkh293. PMC 390282Freely accessible. PMID 14985472.
  15. ↑ Vos, R. A.; Caravas, J.; Hartmann, K.; Jensen, M. A.; Miller, C. (2011). "BIO::Phylo-phyloinformatic analysis using perl". BMC Bioinformatics. 12: 63. doi:10.1186/1471-2105-12-63.
  16. ↑ Huson, D. H.; Richter, D. C.; Rausch, C.; Dezulian, T.; Franz, M.; Rupp, R. (2007). "Dendroscope: an interactive viewer for large phylogenetic trees". BMC Bioinformatics. 8: 460. doi:10.1186/1471-2105-8-460. PMC 2216043Freely accessible. PMID 18034891.
  17. ↑ Bouckaert, Remco; Heled, Joseph (2014-12-08). "DensiTree 2: Seeing Trees Through the Forest". bioRxiv: 012401. doi:10.1101/012401.
  18. ↑ Joachimiak, Marcin P.; Cohen, Fred E. (2002). "JEvTrace: refinement and variations of the evolutionary trace in Java.". Genome Biology. 3 (12). doi:10.1186/gb-2002-3-12-research0077.
  19. ↑ Fernández, Alberto; Gómez, Sergio (2008). "Solving Non-uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms". Journal of Classification. 25 (1): 43–65. doi:10.1007/s00357-008-9004-x.
  20. ↑ Chevenet, F. �O.; Brun, C.; Bañuls, A. L.; Jacq, B.; Christen, R. (2006). "TreeDyn: towards dynamic graphics and annotations for analyses of trees". BMC Bioinformatics. 7: 439. doi:10.1186/1471-2105-7-439. PMC 1615880Freely accessible. PMID 17032440. replacement character in |first1= at position 4 (help)
  21. ↑ Stöver, B. C.; Müller, K. F. (2010). "TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses". BMC Bioinformatics. 11: 7. doi:10.1186/1471-2105-11-7. PMC 2806359Freely accessible. PMID 20051126.
  22. ↑ Page, RDM (1996). "Tree View: An application to display phylogenetic trees on personal computers". Computer Applications in the Biosciences. 12 (4): 357–358. doi:10.1093/bioinformatics/12.4.357. PMID 8902363.
  23. ↑ Francisco, A. P.; Vaz, C.; Monteiro, P.T.; Melo-Cristino, J.; Ramirez, M.; Carrico, J.A. (2012). "PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods". BMC Bioinformatics. 13: 7. doi:10.1186/1471-2105-13-87. PMC 3403920Freely accessible. PMID 22568821.

External links

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