List of phylogenetic tree visualization software
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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.
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Contents
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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] | |
| JEvTrace | A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis. | All | [18] | [9] |
| MultiDendrograms | Application to calculate and plot phylogenetic trees | All | [19] | [10] |
| NJplot | Interactive tree plotter, re-roots, exports as PDF | All | [20] | |
| TreeDyn | Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta information | All | [21] | [11] |
| TreeGraph 2 | Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses | All | [22] | [12] |
| TreeView | Classic treeviewing software that is very highly cited [23] | All | [24] | [13] |
| UGENE | An opensource visual interface for Phylip 3.6 package | All | [25] |
1 "All" refers to Microsoft Windows, Apple OSX and Linux; L=Linux, M=Apple Mac, W=Microsoft Windows
See also
References
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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. http://genomebiology.com/content/3/12/RESEARCH0077.
- ^ 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/.
- ^ 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.
- ^ 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.
- ^ 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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