List of phylogenetic tree visualization software Ilmu Komputer 464 pasar.pts-ptn.net

This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualising phylogenetic trees.

1 Online software
2 Applications
3 See also
4 References
5 External links

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]
Treedraw	HTML5 canvas based phylogenetic tree viewer	[12]
TreeViz	Java tree viewer that does treemaps as well	[13]
T-REX (Webserver)	Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization	[14]	^[7]

Applications

Name	Description	OS¹	Site	Citation
BayesTrees	A program designed to display, analyse and manipulate samples of trees, in particular Bayesian samples.	W	[15]
Dendroscope	An interactive viewer for large phylogenetic trees and networks	All	[16]	^[8]
ETE	A Python toolkit that assists in the visualization of custom phylogenetic tree images (exports as PNG, PDF and SVG).	All	[17]	^[9]
FigTree	Modern treeviewer with coloring and collapsing	All	[18]
Geneious Pro	All-in-one sequence analysis, phylogenetics and molecular cloning application with modern treeviewer	All	[19]
JEvTrace	A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis.	All	[20]	^[10]
MultiDendrograms	Application to calculate and plot phylogenetic trees	All	[21]	^[11]
NJplot	Interactive tree plotter, re-roots, exports as PDF	All	[22]
TreeDyn	Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta information	All	[23]	^[12]
TreeGraph 2	Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses	All	[24]	^[13]
TreeView	Classic treeviewing software that is very highly cited [25]	All	[26]	^[14]
UGENE	An opensource visual interface for Phylip 3.6 package	All	[27]

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

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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2923619/.
^ 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.
^ 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. PMID 22675075.
^ 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2216043/. edit
^ 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 2820433. PMID 20070885. 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC1615880/. edit
^ 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. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2806359/. edit
^ 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.

Daftar/Tabel -- phylogenetic tree visualization software

Contents

Online software

Applications

See also

References

External links