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Daftar/Tabel -- 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

NameDescriptionSiteCitation
ArchaeopteryxJava tree viewer and editor (used to be ATV)[1][1]
Hypergenyvisualise large phylogenies with this hyperbolic tree browser[2] 
InfoViz Tree Toolsthe generic Javascript InfoViz toolkit supports hyperbolic, space and icicle trees[3] 
iTOL - interactive Tree Of Lifeannotate trees with various types of data and export to various graphical formats; scriptable through a batch interface[4][2]
TreeVectorscalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java.[5][3]
jsPhyloSVGopen-source javascript library for rendering highly-extensible, customizable phylogenetic trees.[6][4]
Phylodendrondifferent tree styles, branch styles and output graphical formats[7] 
PhyloExplorera 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]
Phyloviewerweb-based integrated environment for phylogenomic analysis based on the Bioinformatics Portal System[9] 
PhyloWidgetview, edit, and publish phylogenetic trees online; interfaces with databases[10][6]
TREDa 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] 
TreedrawHTML5 canvas based phylogenetic tree viewer[12] 
TreeVizJava 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

NameDescriptionOS1SiteCitation
BayesTreesA program designed to display, analyse and manipulate samples of trees, in particular Bayesian samples.W[15] 
DendroscopeAn interactive viewer for large phylogenetic trees and networksAll[16][8]
ETEA Python toolkit that assists in the visualization of custom phylogenetic tree images (exports as PNG, PDF and SVG).All[17][9]
FigTreeModern treeviewer with coloring and collapsingAll[18] 
Geneious ProAll-in-one sequence analysis, phylogenetics and molecular cloning application with modern treeviewerAll[19] 
JEvTraceA multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis.All[20][10]
MultiDendrogramsApplication to calculate and plot phylogenetic treesAll[21][11]
NJplotInteractive tree plotter, re-roots, exports as PDFAll[22] 
TreeDynVery powerful open-source software for tree manipulation and annotation allowing incorporation of meta informationAll[23][12]
TreeGraph 2Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analysesAll[24][13]
TreeViewClassic treeviewing software that is very highly cited [25]All[26][14]
UGENEAn opensource visual interface for Phylip 3.6 packageAll[27] 

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: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. //www.ncbi.nlm.nih.gov/pmc/articles/P MC2923619/.
  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. ^ 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.
  8. ^ 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/P MC2216043/. edit
  9. ^ 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/1471-210 5/11/24.
  10. ^ 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.
  11. ^ 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/c 8795u6232184423/.
  12. ^ 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/P MC1615880/. edit
  13. ^ 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/P MC2806359/. edit
  14. ^ 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

(Sebelumnya) List of PHP editorsList of phylogenetics software (Berikutnya)