List of phylogenetic tree visualization software

From Wikipedia, the free encyclopedia
Jump to navigation Jump to search

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

Online software[edit]

Name Description Site Citation
Aquapony Javascript tree viewer for Beast. Aquapony
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. [1] [1]
ETE toolkit A Python Environment for Tree Exploration (online treeview) [2] [2]
ggtree An R package for tree visualization and annotation with grammar of graphics supported [3] [3]
Hypergeny visualise large phylogenies with this hyperbolic tree browser [4]
IcyTree Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks. [5] [4]
InfoViz Tree Tools the generic Javascript InfoViz toolkit supports hyperbolic, space and icicle trees [6]
iTOL - interactive Tree Of Life annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface [7] [5]
TreeVector scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java. [8] [6]
jsPhyloSVG open-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for Elsevier's interactive trees [9] [7]
JStree open-source javascript library for viewing and editing phylogenetic trees with HTML5 canvas [10]
OneZoom uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail [11] [8]
PhyD3 interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js [12] [9]
Phylodendron different tree styles, branch styles and output graphical formats [13]
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. [14] [10]
Phylo.io View and compare up to 2 trees side by side with interactive HTML5 visualisations [15] [11]
phylotree.js phylotree.js is a library that extends the popular data visualization framework D3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees [16] [12]
Phyloviewer web-based integrated environment for phylogenomic analysis based on the Bioinformatics Portal System [17][permanent dead link]
PhyloWidget view, edit, and publish phylogenetic trees online; interfaces with databases [18] [13]
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. [19]
Treedraw HTML5 canvas based phylogenetic tree viewer [20]
TreeViz Java tree viewer that does treemaps as well [21]
T-REX (Webserver) Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization [22] [14]
Microreact Link, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines. [23]
PHYLOViZ Online Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees [24] [15]

Desktop Software[edit]

Name Description OS1 Site Citation
ARB An integrated software environment for tree visualisation and annotation. LM [25] [16]
Archaeopteryx Java tree viewer and editor (used to be ATV) [26] [17]
BayesTrees A program designed to display, analyse and manipulate samples of trees, in particular Bayesian samples. W [27]
BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data. W [28]
Bio::Phylo A collection of Perl modules for manipulating and visualizing phylogenetic data. Bio::Philo is one part of a comprehensive suite of Perl biology tools. All [29] [18]
Dendroscope An interactive viewer for large phylogenetic trees and networks All [30] [19]
DensiTree A viewer capable of viewing multiple overlaid trees. All [31] [20]
epos All [32]
FigTree Modern treeviewer with coloring and collapsing All [33]
Geneious Pro All-in-one sequence analysis, phylogenetics and molecular cloning application with modern treeviewer All [34]
JEvTrace A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis. All [35] [21]
MultiDendrograms Interactive open-source application to calculate and plot phylogenetic trees All [36] [22]
NJplot Interactive tree plotter, re-roots, exports as PDF All [37]
Phytools Phylogenetic Tools for Comparative Biology (and Other Things) based in R All [38] [23]
TreeDyn Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta information All [39] [24]
Treevolution Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering, pruning, etc. All [40] [25]
TreeGraph 2 Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses All [41] [26]
TreeView Classic treeviewing software that is very highly cited [42] All [43] [27]
UGENE An opensource visual interface for Phylip 3.6 package All [44]
VectorFriends An integrated sequence analysis software with viewer for phylogenetic trees W [45]
PHYLOViZ Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees All [46] [28]

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

See also[edit]

References[edit]

  1. ^ Zhang H, Gao S, Lercher MJ, Hu S & Chen WH (July 2012). "EvolView, an online tool for visualizing, annotating and managing phylogenetic trees". Nucleic Acids Research. 40 (Web Server issue): W569–72. doi:10.1093/nar/gks576. PMC 3394307. PMID 22695796.
  2. ^ Huerta-Cepas J, Dopazo J, Gabaldón T (January 2010). "ETE: a python Environment for Tree Exploration". BMC Bioinformatics. 11: 24. doi:10.1186/1471-2105-11-24. PMC 2820433. PMID 20070885.
  3. ^ Yu G, Smith DK, Zhu H, Guan Y, Lam TT (January 1, 2017). "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data". Methods in Ecology and Evolution. 8 (1): 28–36. doi:10.1111/2041-210X.12628.
  4. ^ Vaughan TG (August 2017). "IcyTree: rapid browser-based visualization for phylogenetic trees and networks". Bioinformatics. Oxford University Press. 33 (15): 2392–2394. doi:10.1093/bioinformatics/btx155. PMID 28407035.
  5. ^ Letunic I, Bork P (January 2007). "Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation" (PDF). Bioinformatics. Oxford University Press. 23 (1): 127–8. doi:10.1093/bioinformatics/btl529. PMID 17050570.
  6. ^ Pethica R, Barker G, Kovacs T, Gough J (January 2010). "TreeVector: scalable, interactive, phylogenetic trees for the web". PLOS One. 5 (1): e8934. Bibcode:2010PLoSO...5.8934P. doi:10.1371/journal.pone.0008934. PMC 2812488. PMID 20126613.
  7. ^ Smits SA, Ouverney CC (August 2010). Poon AF, ed. "jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web". PLOS One. 5 (8): e12267. Bibcode:2010PLoSO...512267S. doi:10.1371/journal.pone.0012267. PMC 2923619. PMID 20805892.
  8. ^ Rosindell J & Harmon LJ (2012). "OneZoom: a fractal explorer for the tree of life". PLoS Biology. 10 (10): e1001406. doi:10.1371/journal.pbio.1001406. PMC 3472976. PMID 23091419.
  9. ^ Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M (September 2017). "PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization". Bioinformatics. 33 (18): 2946–2947. doi:10.1093/bioinformatics/btx324. PMID 28525531.
  10. ^ Ranwez V, Clairon N, Delsuc F, Pourali S, Auberval N, Diser S, Berry V (May 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. PMC 2695458. PMID 19450253.
  11. ^ Robinson O, Dylus D, Dessimoz C (August 2016). "Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web". Molecular Biology and Evolution. 33 (8): 2163–6. arXiv:1602.04258. doi:10.1093/molbev/msw080. PMC 4948708. PMID 27189561.
  12. ^ Shank SD, Weaver S, Kosakovsky Pond SL (July 2018). "phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics". BMC Bioinformatics. 19 (1): 276. doi:10.1186/s12859-018-2283-2. PMC 6060545. PMID 30045713.
  13. ^ Jordan GE & Piel WH (July 2008). "PhyloWidget: web-based visualizations for the tree of life". Bioinformatics. 24 (14): 1641–2. doi:10.1093/bioinformatics/btn235. PMID 18487241.
  14. ^ Boc A, Diallo AB, Makarenkov V (July 2012). "T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks". Nucleic Acids Research. 40 (Web Server issue): W573–9. doi:10.1093/nar/gks485. PMC 3394261. PMID 22675075.
  15. ^ Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA (July 2016). "PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees". Nucleic Acids Research. 44 (W1): W246–51. doi:10.1093/nar/gkw359. PMC 4987911. PMID 27131357.
  16. ^ Ludwig W, Strunk O, Westram R, Richter L, Meier H, Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004). "ARB: a software environment for sequence data". Nucleic Acids Research. 32 (4): 1363–71. doi:10.1093/nar/gkh293. PMC 390282. PMID 14985472.
  17. ^ Zmasek CM & Eddy SR (April 2001). "ATV: display and manipulation of annotated phylogenetic trees". Bioinformatics. 17 (4): 383–4. doi:10.1093/bioinformatics/17.4.383. PMID 11301314.
  18. ^ Vos RA, Caravas J, Hartmann K, Jensen MA, Miller C (February 2011). "BIO::Phylo-phyloinformatic analysis using perl". BMC Bioinformatics. 12: 63. doi:10.1186/1471-2105-12-63. PMC 3056726. PMID 21352572.
  19. ^ Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R (November 2007). "Dendroscope: An interactive viewer for large phylogenetic trees". BMC Bioinformatics. 8: 460. doi:10.1186/1471-2105-8-460. PMC 2216043. PMID 18034891.
  20. ^ Bouckaert R, Heled J (2014-12-08). "DensiTree 2: Seeing Trees Through the Forest". bioRxiv 012401.
  21. ^ Joachimiak MP, Cohen FE (2002). "JEvTrace: refinement and variations of the evolutionary trace in Java". Genome Biology. 3 (12): research0077.1. doi:10.1186/gb-2002-3-12-research0077.
  22. ^ Fernández A, Gómez S (2008). "Solving Non-uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms". Journal of Classification. 25 (1): 43&ndash, 65. arXiv:cs/0608049. doi:10.1007/s00357-008-9004-x.
  23. ^ Revell, LJ (2012). "phytools: An R package for phylogenetic comparative biology (and other things)". Methods Ecol. Evol. 3 (2): 217–223. doi:10.1111/j.2041-210X.2011.00169.x.
  24. ^ Chevenet F, Brun C, Bañuls AL, Jacq B, Christen R (October 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.
  25. ^ Santamaría R, Therón R (August 2009). "Treevolution: visual analysis of phylogenetic trees". Bioinformatics. 25 (15): 1970–1. doi:10.1093/bioinformatics/btp333. PMID 19470585.
  26. ^ Stöver BC, Müller KF (January 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.
  27. ^ Page RD (August 1996). "TreeView: an application to display phylogenetic trees on personal computers". Computer Applications in the Biosciences. 12 (4): 357–8. doi:10.1093/bioinformatics/12.4.357. PMID 8902363.
  28. ^ Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA (May 2012). "PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods". BMC Bioinformatics. 13: 87. doi:10.1186/1471-2105-13-87. PMC 3403920. PMID 22568821.

External links[edit]