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.

Contents

Online software

Name Description Site Citation
Archaeopteryx Java tree viewer and editor (used to be ATV) [1] [1]
Hypergeny visualise large phylogenies with this hyperbolic tree browser [2]
InfoViz Tree Tools the generic Javascript InfoViz toolkit supports hyperbolic, space and icicle trees [3]
iTOL - interactive Tree Of Life annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface [4] [2]
TreeVector scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java. [5] [3]
jsPhyloSVG open-source javascript library for rendering highly-extensible, customizable phylogenetic trees. [6] [4]
Phylodendron different tree styles, branch styles and output graphical formats [7]
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] [5]
Phyloviewer web-based integrated environment for phylogenomic analysis based on the Bioinformatics Portal System [9]
PhyloWidget view, edit, and publish phylogenetic trees online; interfaces with databases [10] [6]
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. [11]
TreeViz Java tree viewer that does treemaps as well [12]

Applications

Name Description OS1 Site Citation
BayesTrees A program designed to display, analyse and manipulate samples of trees, in particular Bayesian samples. W [13]
Dendroscope An interactive viewer for large phylogenetic trees and networks All [14] [7]
ETE A Python toolkit that assists in the visualization of custom phylogenetic tree images (exports as PNG, PDF and SVG). All [15] [8]
FigTree Modern treeviewer with coloring and collapsing All [16]
Geneious Pro All-in-one sequence analysis, phylogenetics and molecular cloning application with modern treeviewer All [17]
MultiDendrograms Application to calculate and plot phylogenetic trees All [18] [9]
NJplot Interactive tree plotter, re-roots, exports as PDF All [19]
TreeDyn Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta information All [20] [10]
TreeGraph 2 Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses All [21] [11]
TreeView Classic treeviewing software that is very highly cited [22] All [23] [12]
UGENE An opensource visual interface for Phylip 3.6 package All [24]

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

See also

References

  1. ^ Zmasek, CM and 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. ^ Letunic, I and Bork, P (2007). "Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.". Bioinformatics 23 (1): 127–128. doi:10.1093/bioinformatics/btl529. PMID 17050570. 
  3. ^ 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:doi:10.1371/journal.pone.0008934. 
  4. ^ 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 2923619. PMID 20805892. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2923619. 
  5. ^ 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. 
  6. ^ Jordan, EG and Piel, WH (2008). "PhyloWidget: web-based visualizations for the tree of life". Bioinformatics 24 (14): 1641–1642. doi:10.1093/bioinformatics/btn235. PMID 18487241. 
  7. ^ 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 2216043. PMID 18034891. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2216043.  edit
  8. ^ 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. http://www.biomedcentral.com/1471-2105/11/24. 
  9. ^ 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. http://www.springerlink.com/content/c8795u6232184423/. 
  10. ^ 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 1615880. PMID 17032440. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1615880.  edit
  11. ^ 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 2806359. PMID 20051126. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2806359.  edit
  12. ^ Page, RDM (1996). "Tree View: An application to display phylogenetic trees on personal computers". Computer Applications in the Biosciences 12 (4): 357–358. PMID 8902363. 

External links