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List of phylogenetic tree visualization software

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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
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]
jsPhyloSVG open-source javascript library for rendering highly-extensible, customizable phylogenetic trees. [5] [3]
Phylodendron different tree styles, branch styles and output graphical formats [6]
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. [7] [4]
Phyloviewer web-based integrated environment for phylogenomic analysis based on the Bioinformatics Portal System [8]
PhyloWidget view, edit, and publish phylogenetic trees online; interfaces with databases [9] [5]
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. [10]
TreeViz Java tree viewer that does treemaps as well [11]

Applications

Name Description OS1 Site Citation
BayesTrees A program designed to display, analyse and manipulate samples of trees, in particular Bayesian samples. W [12]
Dendroscope An interactive viewer for large phylogenetic trees and networks All [13] [6]
ETE A Python Environment for Tree Exploration. This is a programming library draw and manipulate phylogenetic trees. All [14] [7]
FigTree Modern treeviewer with coloring and collapsing All [15]
Geneious Pro All-in-one sequence analysis, phylogenetics and molecular cloning application with modern treeviewer All [16]
MultiDendrograms Application to calculate and plot phylogenetic trees All [17] [8]
NJplot Interactive tree plotter, re-roots, exports as PDF All [18]
TreeDyn Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta information All [19] [9]
TreeGraph 2 Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses All [20] [10]
TreeView Classic treeviewing software that is very highly cited [21] All [22] [11]
UGENE An opensource visual interface for Phylip 3.6 package 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 and Eddy, SR (2001). "TV: display and manipulation of annotated phylogenetic trees". Bioinformatics. 17 (4): 383–384. PMID 11301314. {{cite journal}}: Text "10.1093/bioinformatics/17.4.383" ignored (help)CS1 maint: multiple names: authors list (link)
  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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ Smits, SA and Ouverney, CC (2010). "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. {{cite journal}}: Cite has empty unknown parameter: |1= (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  4. ^ Ranwez, V et al., WH (2009). "PhyloExplorer: a web server to validate, explore and query phylogenetic trees". BMC Evolutionary Biology. 9 (108). doi:doi:10.1186/1471-2148-9-108. {{cite journal}}: Check |doi= value (help); Cite has empty unknown parameters: |1= and |2= (help)CS1 maint: multiple names: authors list (link)
  5. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1471-2105-8-460, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/1471-2105-8-460 instead.
  7. ^ 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  8. ^ Fernández, Alberto; Gómez, Sergio (2008). "Solving Non-uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms". Journal of Classification. 25: 43–65. doi:10.1007/s00357-008-9004-x.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1471-2105-7-439, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/1471-2105-7-439 instead.
  10. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/1471-2105-11-7, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/1471-2105-11-7 instead.
  11. ^ 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.
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