List of phylogenetic tree visualization software: Difference between revisions

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| an online tool for visualizing, annotating and managing phylogenetic trees.
| an online tool for visualizing, annotating and managing phylogenetic trees.
| [http://www.evolgenius.info/evolview]
| [http://www.evolgenius.info/evolview]
|<ref>{{cite journal|author1=Huangkai Zhang |author2=Shenghan Gao |author3=Martin J. Lercher |author4=Songnian Hu |author5=Wei-Hua Chen |last-author-amp=yes |title=EvolView, an online tool for visualizing, annotating and managing phylogenetic trees|journal=Nucleic Acids Research |volume=40|issue=W1|pages=W569–W572|pmid=22695796|doi=10.1093/nar/gks576|date=Jul 2012 |pmc=3394307}}</ref>
|<ref>{{cite journal | vauthors = Zhang H, Gao S, Lercher MJ, Hu S, Chen WH | title = EvolView, an online tool for visualizing, annotating and managing phylogenetic trees | journal = Nucleic Acids Research | volume = 40 | issue = Web Server issue | pages = W569-72 | date = July 2012 | pmid = 22695796 | pmc = 3394307 | doi = 10.1093/nar/gks576 | last-author-amp = yes }}</ref>
|-
|-
| ETE toolkit
| ETE toolkit
| A Python Environment for Tree Exploration (online treeview)
| A Python Environment for Tree Exploration (online treeview)
| [http://etetoolkit.org/treeview]
| [http://etetoolkit.org/treeview]
|<ref name="biomedcentral.com">{{cite journal | vauthors = Huerta-Cepas J, Dopazo J, Gabaldón T | title = ETE: a python Environment for Tree Exploration | journal = BMC Bioinformatics | volume = 11 | pages = 24 | date = January 2010 | pmid = 20070885 | pmc = 2820433 | doi = 10.1186/1471-2105-11-24 }}</ref>
|<ref name="biomedcentral.com">{{cite journal
|doi=10.1186/1471-2105-11-24
|last1=Huerta-Cepas |first1=Jaime |last2=Dopazo |first2=Joaquin | last3=Gabaldon |first3=Toni
|title=ETE: a python Environment for Tree Exploration
|url=http://www.biomedcentral.com/1471-2105/11/24
|journal=BMC Bioinformatics
|volume=11 |year=2010 |pages=24 |pmid=20070885 |pmc=2820433
}}</ref>
|-
|-
| [https://guangchuangyu.github.io/software/ggtree/ ggtree]
| [https://guangchuangyu.github.io/software/ggtree/ ggtree]
| An R package for tree visualization and annotation with grammar of graphics supported
| An R package for tree visualization and annotation with grammar of graphics supported
| [https://guangchuangyu.github.io/software/ggtree/]
| [https://guangchuangyu.github.io/software/ggtree/]
|<ref name="Methods in Ecology and Evolution">{{cite journal | doi = 10.1111/2041-210X.12628 | last1 = Yu | first1 = Guangchuang | last2 = Smith | first2 = David K. | last3 = Zhu | first3 = Huachen | last4 = Guan | first4 = Yi | last5 = Lam | first5 = Tommy Tsan-Yuk | name-list-format = vanc | title = ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data | journal = Methods in Ecology and Evolution | volume = 8 | issue = 1 | pages = 28–36 | date = January 1, 2017 }}</ref>
|<ref name="Methods in Ecology and Evolution">{{cite journal
|doi=10.1111/2041-210X.12628
|last1=Yu |first1=Guangchuang |last2=Smith |first2=David K. | last3=Zhu |first3=Huachen | last4= Guan|first4=Yi | last5=Lam |first5=Tommy Tsan-Yuk
|title=ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
|url=https://doi.org/10.1111/2041-210X.12628
|journal=Methods in Ecology and Evolution
|volume=8
|issue = 1
|pages=28-36
|date=January 1, 2017
}}</ref>
|-
|-
| Hypergeny
| Hypergeny
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|Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks.
|Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks.
|[https://icytree.org]
|[https://icytree.org]
|<ref>{{cite journal | author=Timothy Vaughan | title=IcyTree: rapid browser-based visualization for phylogenetic trees and networks | url=https://doi.org/10.1093/bioinformatics/btx155 | journal=[[Bioinformatics (journal)|Bioinformatics]] |location=Cambridge |publisher=[[Oxford University Press]] | volume=33 | issue=15 | pages=2392–2394 | doi=10.1093/bioinformatics/btx155 | date=August 1, 2017 | pmid= 28407035}}</ref>
|<ref>{{cite journal | vauthors = Vaughan TG | title = IcyTree: rapid browser-based visualization for phylogenetic trees and networks | journal = Bioinformatics | volume = 33 | issue = 15 | pages = 2392–2394 | date = August 2017 | pmid = 28407035 | doi = 10.1093/bioinformatics/btx155 | publisher = [[Oxford University Press]] }}</ref>
|-
|-
| InfoViz Tree Tools
| InfoViz Tree Tools
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| annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface
| annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface
||[http://itol.embl.de]
||[http://itol.embl.de]
|<ref>{{cite journal |last1=Letunic |first1=Ivica |last2=Bork |first2=Peer |authorlink2=Peer Bork |date=January 1, 2007 |title=Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation |url=http://itol.embl.de/help/17050570.pdf |format=PDF |journal=[[Bioinformatics (journal)|Bioinformatics]] |location=Cambridge |publisher=[[Oxford University Press]] |volume=23 |issue=1 |pages=127–128 |doi=10.1093/bioinformatics/btl529 |issn=1367-4803 |pmid=17050570 |accessdate=2015-07-21}}</ref>
|<ref>{{cite journal | vauthors = Letunic I, Bork P | title = Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation | journal = Bioinformatics | volume = 23 | issue = 1 | pages = 127–8 | date = January 2007 | pmid = 17050570 | doi = 10.1093/bioinformatics/btl529 | url = http://itol.embl.de/help/17050570.pdf | publisher = [[Oxford University Press]] | format = PDF | authorlink2 = Peer Bork }}</ref>
|-
|-
| TreeVector
| TreeVector
| scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java.
| scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java.
||[http://supfam.cs.bris.ac.uk/TreeVector/]
||[http://supfam.cs.bris.ac.uk/TreeVector/]
||<ref>{{cite journal |author=Pethica, R. and Barker, G. and Kovacs, T. and Gough, J. |title=TreeVector: scalable, interactive, phylogenetic trees for the web |journal=PLoS ONE |volume=5 |issue=1 |pages=e8934 |year=2010 |doi=10.1371/journal.pone.0008934 |pmid=20126613 |pmc=2812488|bibcode=2010PLoSO...5.8934P }}</ref>
||<ref>{{cite journal | vauthors = Pethica R, Barker G, Kovacs T, Gough J | title = TreeVector: scalable, interactive, phylogenetic trees for the web | journal = PloS One | volume = 5 | issue = 1 | pages = e8934 | date = January 2010 | pmid = 20126613 | pmc = 2812488 | doi = 10.1371/journal.pone.0008934 | bibcode = 2010PLoSO...5.8934P }}</ref>
|-
|-
| jsPhyloSVG
| jsPhyloSVG
| open-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for [https://www.elsevier.com/authors/author-services/enrichments/interactive-phylogenetic-trees Elsevier's interactive trees]
| open-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for [https://www.elsevier.com/authors/author-services/enrichments/interactive-phylogenetic-trees Elsevier's interactive trees]
||[http://www.jsphylosvg.com/]
||[http://www.jsphylosvg.com/]
|<ref>{{cite journal |author=Smits, SA and Ouverney, CC |editor1-last=Poon |editor1-first=Art F. Y.|title=jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web |journal=PLoS ONE |volume=5 |pages=e12267 |year=2010 |pmid=20805892|issue=8 |pmc=2923619 |doi=10.1371/journal.pone.0012267|bibcode=2010PLoSO...512267S }}</ref>
|<ref>{{cite journal | vauthors = Smits SA, Ouverney CC | title = jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web | journal = PloS One | volume = 5 | issue = 8 | pages = e12267 | date = August 2010 | pmid = 20805892 | pmc = 2923619 | doi = 10.1371/journal.pone.0012267 | editor1-last = Poon | bibcode = 2010PLoSO...512267S | editor1-first = Art F. Y. }}</ref>
|-
|-
|JStree
|JStree
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| uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail
| uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail
||[http://www.onezoom.org/index.htm]
||[http://www.onezoom.org/index.htm]
|<ref>{{cite journal |author1=Rosindell, J |author2=Harmon, LJ |lastauthoramp=yes|title=OneZoom: A Fractal Explorer for the Tree of Life |journal=PLoS Biology |volume=10|issue=10 |year=2012 |doi=10.1371/journal.pbio.1001406 |pmid=23091419 |pmc=3472976 |page=e1001406}}</ref>
|<ref>{{cite journal | vauthors = Rosindell J, Harmon LJ | title = OneZoom: a fractal explorer for the tree of life | journal = PLoS Biology | volume = 10 | issue = 10 | pages = e1001406 | year = 2012 | pmid = 23091419 | pmc = 3472976 | doi = 10.1371/journal.pbio.1001406 | lastauthoramp = yes }}</ref>
|-
|-
| [https://phyd3.bits.vib.be PhyD3]
| [https://phyd3.bits.vib.be PhyD3]
| interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in [[D3.js]]
| interactive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in [[D3.js]]
||[https://phyd3.bits.vib.be]
||[https://phyd3.bits.vib.be]
|<ref>{{cite journal|author1=Kreft, L |author2=Botzki, A |author3=Coppens, F |author4=Vandepoele, K |author5=Van Bel, M |title=PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization |journal=Bioinformatics |year=2017 |doi=10.1093/bioinformatics/btx324 |pmid=28525531 |url=https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx324/3835380/PhyD3-a-phylogenetic-tree-viewer-with-extended}}</ref>
|<ref>{{cite journal | vauthors = Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M | title = PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization | journal = Bioinformatics | volume = 33 | issue = 18 | pages = 2946–2947 | date = September 2017 | pmid = 28525531 | doi = 10.1093/bioinformatics/btx324 | url = https://academic.oup.com/bioinformatics/article-abstract/doi/10.1093/bioinformatics/btx324/3835380/PhyD3-a-phylogenetic-tree-viewer-with-extended }}</ref>
|-
|-
| Phylodendron
| Phylodendron
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| 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.
| 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.
||[https://web.archive.org/web/20110721023225/http://www.ncbi.orthomam.univ-montp2.fr/phyloexplorer/]
||[https://web.archive.org/web/20110721023225/http://www.ncbi.orthomam.univ-montp2.fr/phyloexplorer/]
|<ref>{{cite journal |author=Ranwez, V et al., WH|title=PhyloExplorer: a web server to validate, explore and query phylogenetic trees |series=9 |journal=BMC Evolutionary Biology |volume=9|year=2009 |pages=108 |doi=10.1186/1471-2148-9-108 |pmid=19450253 |pmc=2695458}}</ref>
|<ref>{{cite journal | vauthors = Ranwez V, Clairon N, Delsuc F, Pourali S, Auberval N, Diser S, Berry V | title = PhyloExplorer: a web server to validate, explore and query phylogenetic trees | journal = BMC Evolutionary Biology | volume = 9 | pages = 108 | date = May 2009 | pmid = 19450253 | pmc = 2695458 | doi = 10.1186/1471-2148-9-108 | series = 9 }}</ref>
|-
|-
| [http://phylo.io Phylo.io]
| [http://phylo.io Phylo.io]
| View and compare up to 2 trees side by side with interactive HTML5 visualisations
| View and compare up to 2 trees side by side with interactive HTML5 visualisations
|[http://phylo.io/]
|[http://phylo.io/]
|<ref>{{cite journal|last1=Robinson|first1=Oscar|last2=Dylus|first2=David|title=Phylo.io: interactive viewing and comparison of large phylogenetic trees on the web|journal=Molecular Biology and Evolution|date=2016|doi=10.1093/molbev/msw080|url=http://mbe.oxfordjournals.org/content/early/2016/04/19/molbev.msw080.abstract|accessdate=21 April 2016|pmid=27189561|pmc=4948708|volume=33|issue=8|pages=2163–6|arxiv=1602.04258}}</ref>
|<ref>{{cite journal | vauthors = Robinson O, Dylus D, Dessimoz C | title = Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web | journal = Molecular Biology and Evolution | volume = 33 | issue = 8 | pages = 2163–6 | date = August 2016 | pmid = 27189561 | pmc = 4948708 | doi = 10.1093/molbev/msw080 | arxiv = 1602.04258 }}</ref>
|-
|-
|[http://phylotree.hyphy.org phylotree.js]
|[http://phylotree.hyphy.org 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
|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
|[http://phylotree.hyphy.org]
|[http://phylotree.hyphy.org]
|<ref>{{Cite journal|last=Shank|first=Stephen D.|last2=Weaver|first2=Steven|last3=Kosakovsky Pond|first3=Sergei L.|date=2018-07-25|title=phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics|url=https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2283-2|journal=BMC Bioinformatics|language=En|volume=19|issue=1|doi=10.1186/s12859-018-2283-2|issn=1471-2105|pmc=PMC6060545|pmid=30045713}}</ref>
|<ref>{{cite journal | vauthors = Shank SD, Weaver S, Kosakovsky Pond SL | title = phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics | language = En | journal = BMC Bioinformatics | volume = 19 | issue = 1 | pages = 276 | date = July 2018 | pmid = 30045713 | pmc = 6060545 | doi = 10.1186/s12859-018-2283-2 }}</ref>
|-
|-
| Phyloviewer
| Phyloviewer
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| PhyloWidget
| PhyloWidget
| view, edit, and publish phylogenetic trees online; interfaces with databases ||[http://www.phylowidget.org/]
| view, edit, and publish phylogenetic trees online; interfaces with databases ||[http://www.phylowidget.org/]
|<ref>{{cite journal |author1=Jordan, EG |author2=Piel, WH |lastauthoramp=yes|title=PhyloWidget: web-based visualizations for the tree of life |journal=Bioinformatics |volume=24 |pages=1641–1642 |year=2008 |pmid=18487241 |issue=14 |doi=10.1093/bioinformatics/btn235}}</ref>
|<ref>{{cite journal | vauthors = Jordan GE, Piel WH | title = PhyloWidget: web-based visualizations for the tree of life | journal = Bioinformatics | volume = 24 | issue = 14 | pages = 1641–2 | date = July 2008 | pmid = 18487241 | doi = 10.1093/bioinformatics/btn235 | lastauthoramp = yes }}</ref>
|-
|-
| TRED
| TRED
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| [[T-REX (Webserver)]]
| [[T-REX (Webserver)]]
| Tree inference and visualization (hierarchical, radial and axial tree views), [[Horizontal gene transfer]] detection and HGT network visualization ||[http://www.trex.uqam.ca/]
| Tree inference and visualization (hierarchical, radial and axial tree views), [[Horizontal gene transfer]] detection and HGT network visualization ||[http://www.trex.uqam.ca/]
|<ref>{{cite journal |doi=10.1093/nar/gks485 |vauthors=Boc A, Diallo Alpha B, Makarenkov V |title=T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks |journal=Nucleic Acids Research |volume= 40|pages=W573–W579. |year=2012 |pmid=22675075 |issue=Web Server issue |pmc=3394261}}</ref>
|<ref>{{cite journal | vauthors = Boc A, Diallo AB, Makarenkov V | title = T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks | journal = Nucleic Acids Research | volume = 40 | issue = Web Server issue | pages = W573-9 | date = July 2012 | pmid = 22675075 | pmc = 3394261 | doi = 10.1093/nar/gks485 }}</ref>
|-
|-
|Microreact
|Microreact
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|Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees
|Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees
|[https://online.phyloviz.net]
|[https://online.phyloviz.net]
|<ref>{{cite journal|title = PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees|url = http://nar.oxfordjournals.org/content/early/2016/04/29/nar.gkw359.abstract|journal = Nucleic Acids Research|date = 2016-04-21|pmc =4987911|pmid = 27131357 |volume = 16|issue = 1|pages = W246–W251|doi =10.1093/nar/gkw359|language = En|first = Bruno |last = Ribeiro-Gonçalves|first2 = Alexandre |last2 = P. Francisco|first3 = Cátia|last3 = Vaz|first4 = Mário|last4 = Ramirez | first5 = João| last5= André Carriço}}</ref>
|<ref>{{cite journal | vauthors = Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA | title = PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees | language = En | journal = Nucleic Acids Research | volume = 44 | issue = W1 | pages = W246-51 | date = July 2016 | pmid = 27131357 | pmc = 4987911 | doi = 10.1093/nar/gkw359 }}</ref>
|}
|}


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|-
|-
| ARB
| ARB
| An integrated software environment for tree visualisation and annotation.||LM||[http://www.arb-home.de/]||<ref name="pmid14985472">{{cite journal
| An integrated software environment for tree visualisation and annotation.||LM||[http://www.arb-home.de/]||<ref name="pmid14985472">{{cite journal | vauthors = 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 | title = ARB: a software environment for sequence data | journal = Nucleic Acids Research | volume = 32 | issue = 4 | pages = 1363–71 | year = 2004 | pmid = 14985472 | pmc = 390282 | doi = 10.1093/nar/gkh293 }}</ref>
|vauthors=Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, 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
|title=ARB: a software environment for sequence data
|journal=Nucleic Acids Res.
|volume=32
|issue=4
|pages=1363–71
|year=2004
|pmid=14985472
|pmc=390282
|doi=10.1093/nar/gkh293
|url=
}}</ref>
|-
|-
| [[Archaeopteryx (evolutionary tree visualization and analysis)|Archaeopteryx]]
| [[Archaeopteryx (evolutionary tree visualization and analysis)|Archaeopteryx]]
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||
||
||[https://sites.google.com/site/cmzmasek/home/software/archaeopteryx]
||[https://sites.google.com/site/cmzmasek/home/software/archaeopteryx]
|<ref>{{cite journal |doi=10.1093/bioinformatics/17.4.383 |author1=Zmasek, CM |author2=Eddy, SR |lastauthoramp=yes|title=TV: display and manipulation of annotated phylogenetic trees |journal=Bioinformatics |volume=17 |pages=383–384 |year=2001 |pmid=11301314 |issue=4}}</ref>
|<ref>{{cite journal | vauthors = Zmasek CM, Eddy SR | title = ATV: display and manipulation of annotated phylogenetic trees | journal = Bioinformatics | volume = 17 | issue = 4 | pages = 383–4 | date = April 2001 | pmid = 11301314 | doi = 10.1093/bioinformatics/17.4.383 | lastauthoramp = yes }}</ref>
|-
|-
| BayesTrees
| BayesTrees
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|-
|-
| Bio::Phylo
| Bio::Phylo
| A collection of Perl modules for manipulating and visualizing phylogenetic data. Bio::Philo is one part of a comprehensive suite of [[BioPerl|Perl biology tools]]. ||All|| [https://metacpan.org/pod/Bio::Phylo]||<ref>{{Cite journal | doi = 10.1186/1471-2105-12-63| title = BIO::Phylo-phyloinformatic analysis using perl| journal = BMC Bioinformatics| volume = 12| pages = 63| year = 2011| last1 = Vos | first1 = R. A. | last2 = Caravas | first2 = J. | last3 = Hartmann | first3 = K. | last4 = Jensen | first4 = M. A. | last5 = Miller | first5 = C. | pmid=21352572 | pmc=3056726}}</ref>
| A collection of Perl modules for manipulating and visualizing phylogenetic data. Bio::Philo is one part of a comprehensive suite of [[BioPerl|Perl biology tools]]. ||All|| [https://metacpan.org/pod/Bio::Phylo]||<ref>{{cite journal | vauthors = Vos RA, Caravas J, Hartmann K, Jensen MA, Miller C | title = BIO::Phylo-phyloinformatic analysis using perl | journal = BMC Bioinformatics | volume = 12 | pages = 63 | date = February 2011 | pmid = 21352572 | pmc = 3056726 | doi = 10.1186/1471-2105-12-63 }}</ref>
|-
|-
| [[Dendroscope]]
| [[Dendroscope]]
| An interactive viewer for large phylogenetic trees and networks ||All||[http://www-ab.informatik.uni-tuebingen.de/software/dendroscope/welcome.html]||<ref>{{Cite journal | last1 = Huson | first1 = D. H. | last2 = Richter | first2 = D. C. | last3 = Rausch | first3 = C. | last4 = Dezulian | first4 = T. | last5 = Franz | first5 = M. | last6 = Rupp | first6 = R. | title = Dendroscope: an interactive viewer for large phylogenetic trees | journal = BMC Bioinformatics | volume = 8 | pages = 460 | year = 2007 | pmid = 18034891 | pmc = 2216043 | 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 journal | vauthors = Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R | title = Dendroscope: An interactive viewer for large phylogenetic trees | journal = BMC Bioinformatics | volume = 8 | pages = 460 | date = November 2007 | pmid = 18034891 | pmc = 2216043 | doi = 10.1186/1471-2105-8-460 }}</ref>
|-
|-
|DensiTree
|DensiTree
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|All
|All
|[https://github.com/rbouckaert/DensiTree]
|[https://github.com/rbouckaert/DensiTree]
|<ref>{{cite biorxiv|title = DensiTree 2: Seeing Trees Through the Forest|biorxiv = 012401|date = 2014-12-08|first = Remco|last = Bouckaert|first2 = Joseph|last2 = Heled}}</ref>
|<ref>{{cite biorxiv|title = DensiTree 2: Seeing Trees Through the Forest|biorxiv = 012401|date = 2014-12-08|first = Remco|last = Bouckaert|first2 = Joseph|last2 = Heled | name-list-format = vanc }}</ref>
|-
|-
| epos
| epos
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|-
|-
| JEvTrace
| JEvTrace
| A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive [https://www.ncbi.nlm.nih.gov/pubmed/8609628 Evolutionary Trace] and other phylogeny inspired analysis.||All||[http://compbio.berkeley.edu/people/marcin/jevtrace/index.html]||<ref>{{
| A multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive [https://www.ncbi.nlm.nih.gov/pubmed/8609628 Evolutionary Trace] and other phylogeny inspired analysis.||All||[http://compbio.berkeley.edu/people/marcin/jevtrace/index.html]||<ref>{{cite journal | doi = 10.1186/gb-2002-3-12-research0077 | last1 = Joachimiak | first1 = Marcin P. | last2 = Cohen | first2 = Fred E. | name-list-format = vanc | title = JEvTrace: refinement and variations of the evolutionary trace in Java. | url = http://genomebiology.com/content/3/12/RESEARCH0077 | journal = Genome Biology | volume = 3 | year = 2002 | issue = 12 | page = research0077.1 }}</ref>
cite journal
|doi=10.1186/gb-2002-3-12-research0077
|last1=Joachimiak |first1=Marcin P. |last2=Cohen |first2=Fred E.
|title=JEvTrace: refinement and variations of the evolutionary trace in Java.
|url=http://genomebiology.com/content/3/12/RESEARCH0077
|journal=Genome Biology
|volume=3 |year=2002
|issue=12
|page=research0077.1
}}</ref>
|-
|-
| MultiDendrograms
| MultiDendrograms
| Interactive open-source application to calculate and plot phylogenetic trees ||All||[http://deim.urv.cat/~sergio.gomez/multidendrograms.php]||<ref>{{cite journal
| Interactive open-source application to calculate and plot phylogenetic trees ||All||[http://deim.urv.cat/~sergio.gomez/multidendrograms.php]||<ref>{{cite journal | doi = 10.1007/s00357-008-9004-x | last1 = Fernández | first1 = Alberto | last2 = Gómez | first2 = Sergio | name-list-format = vanc | title = Solving Non-uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms | url = http://www.springerlink.com/content/c8795u6232184423/ | journal = Journal of Classification | volume = 25 | year = 2008 | issue = 1 | pages = 43&ndash;65 | arxiv = cs/0608049 }}</ref>
|doi=10.1007/s00357-008-9004-x
|last1=Fern&aacute;ndez |first1=Alberto |last2=G&oacute;mez |first2=Sergio
|title=Solving Non-uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms
|url=http://www.springerlink.com/content/c8795u6232184423/
|journal=Journal of Classification
|volume=25 |year=2008
|issue=1 |pages=43&ndash;65
|arxiv=cs/0608049}}</ref>
|-
|-
| NJplot
| NJplot
Line 229: Line 182:
|-
|-
| TreeDyn
| TreeDyn
| Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta information||All||[http://www.treedyn.org/]||<ref>{{Cite journal | last1 = Chevenet | first1 = F. | last2 = Brun | first2 = C. | last3 = Bañuls | first3 = A. L. | last4 = Jacq | first4 = B. | last5 = Christen | first5 = R. | title = TreeDyn: towards dynamic graphics and annotations for analyses of trees | journal = BMC Bioinformatics | volume = 7 | pages = 439 | year = 2006 | doi = 10.1186/1471-2105-7-439 | pmc = 1615880 | pmid = 17032440 }}</ref>
| Very powerful open-source software for tree manipulation and annotation allowing incorporation of meta information||All||[http://www.treedyn.org/]||<ref>{{cite journal | vauthors = Chevenet F, Brun C, Bañuls AL, Jacq B, Christen R | title = TreeDyn: towards dynamic graphics and annotations for analyses of trees | journal = BMC Bioinformatics | volume = 7 | pages = 439 | date = October 2006 | pmid = 17032440 | pmc = 1615880 | doi = 10.1186/1471-2105-7-439 }}</ref>
|-
|-
| Treevolution
| Treevolution
| Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering, pruning, etc.||All||[http://vis.usal.es/treevolution/]||<ref>{{Cite journal | last1 = Santamaría | first1 = R. | last2 = Therón | first2 = R. | title = R. Treevolution: visual analysis of phylogenetic trees | journal = Bioinformatics | volume = 25 | issue = 15 | pages = 1970–1971 | year = 2009 | pmid = 19470585 | pmc = | doi = 10.1093/bioinformatics/btp333}}</ref>
| Open-source tool for circular visualization with section and ring distortion and several other features such as branch clustering, pruning, etc.||All||[http://vis.usal.es/treevolution/]||<ref>{{cite journal | vauthors = Santamaría R, Therón R | title = Treevolution: visual analysis of phylogenetic trees | journal = Bioinformatics | volume = 25 | issue = 15 | pages = 1970–1 | date = August 2009 | pmid = 19470585 | pmc = | doi = 10.1093/bioinformatics/btp333 }}</ref>
|-
|-
| TreeGraph 2
| TreeGraph 2
| Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses||All||[http://treegraph.bioinfweb.info/]||<ref>{{Cite journal | last1 = Stöver | first1 = B. C. | last2 = Müller | first2 = K. F. | title = TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses | journal = BMC Bioinformatics | volume = 11 | pages = 7 | year = 2010 | pmid = 20051126 | pmc = 2806359 | doi = 10.1186/1471-2105-11-7}}</ref>
| Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analyses||All||[http://treegraph.bioinfweb.info/]||<ref>{{cite journal | vauthors = Stöver BC, Müller KF | title = TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses | journal = BMC Bioinformatics | volume = 11 | pages = 7 | date = January 2010 | pmid = 20051126 | pmc = 2806359 | doi = 10.1186/1471-2105-11-7 }}</ref>
|-
|-
| TreeView
| TreeView
| Classic treeviewing software that is very highly cited [http://www.lab-times.org/labtimes/issues/lt2008/lt03/lt_2008_03_34_36.pdf]||All||[http://taxonomy.zoology.gla.ac.uk/rod/treeview.html]||<ref>{{cite journal |author=Page, RDM |title=Tree View: An application to display phylogenetic trees on personal computers |journal=Computer Applications in the Biosciences |volume=12 |pages=357–358 |year=1996 |pmid=8902363 |issue=4 |doi=10.1093/bioinformatics/12.4.357}}</ref>
| Classic treeviewing software that is very highly cited [http://www.lab-times.org/labtimes/issues/lt2008/lt03/lt_2008_03_34_36.pdf]||All||[http://taxonomy.zoology.gla.ac.uk/rod/treeview.html]||<ref>{{cite journal | vauthors = Page RD | title = TreeView: an application to display phylogenetic trees on personal computers | journal = Computer Applications in the Biosciences | volume = 12 | issue = 4 | pages = 357–8 | date = August 1996 | pmid = 8902363 | doi = 10.1093/bioinformatics/12.4.357 }}</ref>
|-
|-
| [[UGENE]]
| [[UGENE]]
Line 247: Line 200:
|-
|-
| [[PHYLOViZ]]
| [[PHYLOViZ]]
| Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees ||All||[http://www.phyloviz.net]||<ref>{{Cite journal | last1 = Francisco | first1 = A. P. | last2 = Vaz | first2 = C.| last3 = Monteiro | first3 = P.T. | last4 = Melo-Cristino | first4 = J. |last5 = Ramirez | first5 = M. | last6 = Carrico | first6 = J.A. | title = PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods | journal = BMC Bioinformatics | volume = 13 | pages = 7 | year = 2012 | pmid = 22568821 | pmc = 3403920 | doi = 10.1186/1471-2105-13-87}}</ref>
| Phylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning Trees ||All||[http://www.phyloviz.net]||<ref>{{cite journal | vauthors = Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carriço JA | title = PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods | journal = BMC Bioinformatics | volume = 13 | pages = 87 | date = May 2012 | pmid = 22568821 | pmc = 3403920 | doi = 10.1186/1471-2105-13-87 }}</ref>
|}
|}


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


==See also==
== See also ==
*[[List of phylogenetics software]]
*[[List of phylogenetics software]]


==References==
== References ==
{{reflist}}
{{reflist}}


==External links==
== External links ==
*[https://web.archive.org/web/20090819083843/http://bioinfo.unice.fr/biodiv/Tree_editors.html A 'comprehensive list' of Tree Editors]
*[https://web.archive.org/web/20090819083843/http://bioinfo.unice.fr/biodiv/Tree_editors.html A 'comprehensive list' of Tree Editors]
*[http://www.treedyn.org/Tree_editors.html List of Tree Editors]
*[http://www.treedyn.org/Tree_editors.html List of Tree Editors]

Revision as of 04:04, 1 August 2018

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
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

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

References

  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. {{cite journal}}: Unknown parameter |last-author-amp= ignored (|name-list-style= suggested) (help)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  3. ^ 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. {{cite journal}}: Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)
  4. ^ Vaughan TG (August 2017). "IcyTree: rapid browser-based visualization for phylogenetic trees and networks". Bioinformatics. 33 (15). Oxford University Press: 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. 23 (1). Oxford University Press: 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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. {{cite journal}}: Unknown parameter |lastauthoramp= ignored (|name-list-style= suggested) (help)CS1 maint: unflagged free DOI (link)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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. {{cite journal}}: Unknown parameter |lastauthoramp= ignored (|name-list-style= suggested) (help)
  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. {{cite journal}}: Unknown parameter |lastauthoramp= ignored (|name-list-style= suggested) (help)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  20. ^ Bouckaert, Remco; Heled, Joseph (2014-12-08). "DensiTree 2: Seeing Trees Through the Forest". bioRxiv 012401. {{cite bioRxiv}}: Check |biorxiv= value (help); Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)
  21. ^ 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. {{cite journal}}: Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)CS1 maint: unflagged free DOI (link)
  22. ^ Fernández, Alberto; Gómez, Sergio (2008). "Solving Non-uniqueness in Agglomerative Hierarchical Clustering Using Multidendrograms". Journal of Classification. 25 (1): 43–65. arXiv:cs/0608049. doi:10.1007/s00357-008-9004-x. {{cite journal}}: Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)

External links

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