Biology:List of phylogenetic tree visualization software

From HandWiki
Short description: Wikipedia list article

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 Citation
Aquapony Javascript tree viewer for Beast [1]
ETE toolkit Tree Viewer an online tool for phylogenetic tree view (newick format) that allows multiple sequence alignments to be shown together with the trees (fasta format) [2]
EvolView an online tool for visualizing, annotating and managing phylogenetic trees [3]
IcyTree Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks [4]
Iroki Automatic customization and visualization of phylogenetic trees [5]
iTOL - interactive Tree Of Life annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface
Microreact Link, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines [6]
OneZoom uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail [7]
pangolin Assign a given sample genomic sequence of SARS-CoV-2 to its lineage [8]
Phylo.io View and compare up to 2 trees side by side with interactive HTML5 visualisations [9]
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. [10]
PHYLOViZ Online Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees [11]
PhyloWidget view, edit, and publish phylogenetic trees online; interfaces with databases [12]
T-REX (Webserver) Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization [13]
TidyTree A client-side HTML5/SVG Phylogenetic Tree Renderer, based on D3.js [14]
TreeVector scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java [15]

Desktop software

Name Description OS1 Citation
ARB An integrated software environment for tree visualisation and annotation LM [16]
Archaeopteryx Java tree viewer and editor (used to be ATV) [17]
BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence data W [18]
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 [19]
Dendroscope An interactive viewer for large phylogenetic trees and networks All [20]
DensiTree A viewer capable of viewing multiple overlaid trees. All [21]
FigTree Simple Java tree viewer able to read newick and nexus tree files. Can be used to color branches and produce vector artwork. All [22]
JEvTrace A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace[23] and other phylogeny-inspired analysis. All [24]
MEGA Software for statistical analysis of molecular evolution. It includes different tree visualization features All [25]
MultiDendrograms Interactive open-source application to calculate and plot phylogenetic trees All [26]
PHYLOViZ Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees All [27]
SplitsTree Software for viewing trees, cladograms, NeighborNets, and other graphs All [28]
TreeDyn Open-source software for tree manipulation and annotation allowing incorporation of meta information All [29]
Treevolution Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering and pruning All [30]
TreeGraph 2 Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses All [31]
TreeView Treeviewing software All [32][33]
UGENE An opensource visual interface for Phylip 3.6 package All [34]

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

Libraries

Name Language Description Citation
ggtree R An R package for tree visualization and annotation with grammar of graphics supported [35]
jsPhyloSVG Javascript open-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for Elsevier's interactive trees
PhyD3 Javascript interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js [36]
phylotree.js Javascript 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 [37]
PhyloPlots.jl Julia PhyloPlots.jl is a julia package for plotting phylogenetic trees and networks, integrated with PhyloNetworks.jl [38]
Phytools R Phylogenetic Tools for Comparative Biology (and Other Things) based in R [39]
toytree Python Toytree: A minimalist tree visualization and manipulation library for Python [40]

See also

References

  1. ↑ Cazaux, Bastien; Castel, Guillaume; Rivals, Eric (2019-01-14). "AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees". Bioinformatics 35 (17): 3163–3165. doi:10.1093/bioinformatics/btz011. ISSN 1367-4803. PMID 30649190. https://hal-lirmm.ccsd.cnrs.fr/lirmm-01980994/file/aquapony-ms.pdf. 
  2. ↑ "ETE: a python Environment for Tree Exploration". BMC Bioinformatics 11: 24. January 2010. doi:10.1186/1471-2105-11-24. PMID 20070885. 
  3. ↑ "EvolView, an online tool for visualizing, annotating and managing phylogenetic trees". Nucleic Acids Research 40 (Web Server issue): W569–72. July 2012. doi:10.1093/nar/gks576. PMID 22695796. 
  4. ↑ "IcyTree: rapid browser-based visualization for phylogenetic trees and networks". Bioinformatics 33 (15): 2392–2394. August 2017. doi:10.1093/bioinformatics/btx155. PMID 28407035. 
  5. ↑ "Iroki: automatic customization and visualization of phylogenetic trees". PeerJ 8 (e8584): e8584. February 2020. doi:10.7717/peerj.8584. PMID 32149022. 
  6. ↑ Argimón, Silvia; Abudahab, Khalil; Goater, Richard J. E.; Fedosejev, Artemij; Bhai, Jyothish; Glasner, Corinna; Feil, Edward J.; Holden, Matthew T. G. et al. (2016-11-30). "Microreact: visualizing and sharing data for genomic epidemiology and phylogeography". Microbial Genomics 2 (11): e000093. doi:10.1099/mgen.0.000093. ISSN 2057-5858. PMID 28348833. 
  7. ↑ "OneZoom: a fractal explorer for the tree of life". PLOS Biology 10 (10): e1001406. 2012. doi:10.1371/journal.pbio.1001406. PMID 23091419. 
  8. ↑ Rambaut, A. et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMID 32669681. 
  9. ↑ "Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web". Molecular Biology and Evolution 33 (8): 2163–6. August 2016. doi:10.1093/molbev/msw080. PMID 27189561. Bibcode: 2016arXiv160204258R. 
  10. ↑ "PhyloExplorer: a web server to validate, explore and query phylogenetic trees". BMC Evolutionary Biology. 9 9: 108. May 2009. doi:10.1186/1471-2148-9-108. PMID 19450253. 
  11. ↑ "PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees" (in En). Nucleic Acids Research 44 (W1): W246–51. July 2016. doi:10.1093/nar/gkw359. PMID 27131357. 
  12. ↑ "PhyloWidget: web-based visualizations for the tree of life". Bioinformatics 24 (14): 1641–2. July 2008. doi:10.1093/bioinformatics/btn235. PMID 18487241. 
  13. ↑ "T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks". Nucleic Acids Research 40 (Web Server issue): W573–9. July 2012. doi:10.1093/nar/gks485. PMID 22675075. 
  14. ↑ Boyles, Anthony (2019). "TidyTree: Uncompromisingly Flexible Phylogenetic Trees". CDC. https://cdcgov.github.io/TidyTree/app/. 
  15. ↑ "TreeVector: scalable, interactive, phylogenetic trees for the web". PLOS ONE 5 (1): e8934. January 2010. doi:10.1371/journal.pone.0008934. PMID 20126613. Bibcode: 2010PLoSO...5.8934P. 
  16. ↑ "ARB: a software environment for sequence data". Nucleic Acids Research 32 (4): 1363–71. 2004. doi:10.1093/nar/gkh293. PMID 14985472. 
  17. ↑ "ATV: display and manipulation of annotated phylogenetic trees". Bioinformatics 17 (4): 383–4. April 2001. doi:10.1093/bioinformatics/17.4.383. PMID 11301314. 
  18. ↑ BioNumerics protocols used by Pulsenet
  19. ↑ "BIO::Phylo-phyloinformatic analysis using perl". BMC Bioinformatics 12: 63. February 2011. doi:10.1186/1471-2105-12-63. PMID 21352572. 
  20. ↑ "Dendroscope: An interactive viewer for large phylogenetic trees". BMC Bioinformatics 8: 460. November 2007. doi:10.1186/1471-2105-8-460. PMID 18034891. 
  21. ↑ Bouckaert R, Heled J (2014-12-08). "DensiTree 2: Seeing Trees Through the Forest". bioRxiv 10.1101/012401.
  22. ↑ Rambaut A. 2018. FigTree 1.4.4 github.com accessed 17 April 2018
  23. ↑ Lichtarge, O.; Bourne, H. R.; Cohen, F. E. (1996-03-29). "An evolutionary trace method defines binding surfaces common to protein families". Journal of Molecular Biology 257 (2): 342–358. doi:10.1006/jmbi.1996.0167. ISSN 0022-2836. PMID 8609628. 
  24. ↑ Joachimiak, Marcin P.; Cohen, Fred E. (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. PMID 12537566. 
  25. ↑ "MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms". Molecular Biology and Evolution 35 (6): 1547–1549. June 2018. doi:10.1093/molbev/msy096. PMID 29722887. 
  26. ↑ 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. 
  27. ↑ "PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods". BMC Bioinformatics 13: 87. May 2012. doi:10.1186/1471-2105-13-87. PMID 22568821. 
  28. ↑ Huson, D. H.; D. Bryant (2006). "Application of Phylogenetic Networks in Evolutionary Studies". Mol. Biol. Evol. 23 (2): 254–267. doi:10.1093/molbev/msj030. PMID 16221896. 
  29. ↑ "TreeDyn: towards dynamic graphics and annotations for analyses of trees". BMC Bioinformatics 7: 439. October 2006. doi:10.1186/1471-2105-7-439. PMID 17032440. 
  30. ↑ "Treevolution: visual analysis of phylogenetic trees". Bioinformatics 25 (15): 1970–1. August 2009. doi:10.1093/bioinformatics/btp333. PMID 19470585. 
  31. ↑ "TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses". BMC Bioinformatics 11: 7. January 2010. doi:10.1186/1471-2105-11-7. PMID 20051126. 
  32. ↑ "Publication Analysis 1996-2006 Evolutionary Biology". http://www.lab-times.org/labtimes/issues/lt2008/lt03/lt_2008_03_34_36.pdf. 
  33. ↑ "TreeView: an application to display phylogenetic trees on personal computers". Computer Applications in the Biosciences 12 (4): 357–8. August 1996. doi:10.1093/bioinformatics/12.4.357. PMID 8902363. 
  34. ↑ "Unipro UGENE: a unified bioinformatics toolkit". Bioinformatics 28 (8): 1166–7. 2012. doi:10.1093/bioinformatics/bts091. PMID 22368248. 
  35. ↑ Yu, Guangchuang; Smith, David K.; Zhu, Huachen; Guan, Yi; Lam, Tommy Tsan-Yuk (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. https://semanticscholar.org/paper/2a78ae3ca4519222f21b2d05057dec80684bde8c. 
  36. ↑ "PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization". Bioinformatics 33 (18): 2946–2947. September 2017. doi:10.1093/bioinformatics/btx324. PMID 28525531. 
  37. ↑ "phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics" (in En). BMC Bioinformatics 19 (1): 276. July 2018. doi:10.1186/s12859-018-2283-2. PMID 30045713. 
  38. ↑ "PhyloNetworks: A Package for phylogenetic networks" (in En). Molecular Biology and Evolution 34 (12): 3292–3298. 2017. doi:10.1093/molbev/msx235. PMID 28961984. https://academic.oup.com/mbe/article/34/12/3292/4103410. 
  39. ↑ 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. 
  40. ↑ Eaton, DAR (2019). "Toytree: A minimalist tree visualization and manipulation library for Python". Methods Ecol. Evol. 11 (1): 187–191. doi:10.1111/2041-210X.13313. 

External links



Retrieved from "https://handwiki.org/wiki/index.php?title=Biology:List_of_phylogenetic_tree_visualization_software&oldid=3551365"