List of phylogenetic tree visualization software: Difference between revisions
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| An interactive viewer for large phylogenetic trees and networks ||All||[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html]||<ref>{{cite doi|10.1186/1471-2105-8-460}}</ref> |
| An interactive viewer for large phylogenetic trees and networks ||All||[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html]||<ref>{{cite doi|10.1186/1471-2105-8-460}}</ref> |
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| [http://ete.cgenomics.org ETE] |
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| A Python Environment for Tree Exploration. This is a programming library draw and manipulate phylogenetic trees. || All || [http://ete.cgenomics.org ETE] || <ref>{{cite journal |
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|doi=10.1186/1471-2105-11-24 |
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|last1=Huerta-Cepas |first1=Jaime |last2=Dopazo |first2=Joaquin | last3=Gabaldon |first3=Toni |
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|title=ETE: a python Environment for Tree Exploration |
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|url=http://www.biomedcentral.com/1471-2105/11/24 |
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|journal=BMC Bioinformatics |
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|volume=11 |year=2010 |pages=24 |
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}}</ref> |
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| FigTree |
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Revision as of 14:14, 22 November 2010
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 | ETE | [7] |
| FigTree | Modern treeviewer with coloring and collapsing | All | [14] | |
| Geneious Pro | All-in-one sequence analysis, phylogenetics and molecular cloning application with modern treeviewer | All | [15] | |
| MultiDendrograms | Application to calculate and plot phylogenetic trees | All | [16] | [8] |
| NJplot | Interactive tree plotter, re-roots, exports as PDF | All | [17] | |
| TreeDyn | Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta information | All | [18] | [9] |
| TreeGraph 2 | Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses | All | [19] | [10] |
| TreeView | Classic treeviewing software that is very highly cited [20] | All | [21] | [11] |
| UGENE | An opensource visual interface for Phylip 3.6 package | All | [22] |
1 "All" refers to Microsoft Windows, Apple OSX and Linux; L=Linux, M=Apple Mac, W=Microsoft Windows
External links
See also
References
- ^ 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) - ^ 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) - ^ 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) - ^ 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) - ^ 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) - ^ 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=10.1186/1471-2105-8-460instead. - ^ 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) - ^ 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) - ^ 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=10.1186/1471-2105-7-439instead. - ^ 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=10.1186/1471-2105-11-7instead. - ^ 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.