Visualizing Phylogenetic Trees Using TreeView

Roderic D.M. Page1

1 University of Glasgow, Glasgow, Scotland
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 6.2
DOI:  10.1002/0471250953.bi0602s01
Online Posting Date:  August, 2002
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Abstract

TreeView provides a simple way to view the phylogenetic trees produced by a range of programs, such as PAUP*, PHYLIP, TREE‐PUZZLE, and ClustalX. While some phylogenetic programs (such as the Macintosh version of PAUP*) have excellent tree printing facilities, many programs do not have the ability to generate publication quality trees. TreeView addresses this need. The program can read and write a range of tree file formats, display trees in a variety of styles, print trees, and save the tree as a graphic file. Protocols in this unit cover both displaying and printing a tree. Support protocols describe how to download and install TreeView, and how to display bootstrap values in trees generated by ClustalX and PAUP*.

     
 
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Table of Contents

  • Basic Protocol 1: Displaying a Phylogenetic Tree
  • Basic Protocol 2: Printing One or More Phylogenetic Trees
  • Support Protocol 1: Obtaining the Treeview Program
  • Support Protocol 2: Obtaining the Treeview X Program
  • Support Protocol 3: Displaying Bootstrap Values in ClustalX Trees
  • Support Protocol 4: Displaying Bootstrap Values in PAUP* Trees
  • Guidelines for Understanding Results
  • Commentary
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
   Maddison, D.R., Swofford, D.L., and Maddison, W.P. 1997. NEXUS: An extensible file format for systematic information. Syst. Biol. 46:590‐621.
   Page, R.D.M. 1996. TreeView: An application to display phylogenetic trees on personal computers. CABIOS 12:357‐8.
   Perrière, G. and Gouy, M. 1996. WWW‐Query: An on‐line retrieval system for biological sequence banks. Biochimie 78:364‐369.
   Strimmer, K. and von Haeseler, A. 1996. Quartet puzzling: A quartet maximum‐likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964‐969.
   Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876‐4882.
   Zmasek, C.M. and Eddy, S.R. 2001. ATV: Display and manipulation of annotated phylogenetic trees. Bioinformatics 17:383‐384.
Key References
   Page, 1996. See above.
  A short description of the program, together with example screenshots. Since this article was written, TreeView has been ported to the Unix operating system (http://darwin.zoology.gla.ac.uk/∼rpage/treeviewx/).
Internet Resources
   http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
  TreeView Web site.
   http://darwin.zoology.gla.ac.uk/∼rpage/treeviewx/
  TreeView X Web site. This program is a Unix port of TreeView.
   http://evolution.genetics.washington.edu/phylip/software.html#Plotting
  Joe Felsenstein's list of tree‐drawing programs.
   http://rdp.cme.msu.edu/docs/treeview_newick.html
  Gary Olsen's description of the Newick tree format.
   http://evolution.genetics.washington.edu/phylip/newicktree.html
  Joe Felsenstein's description of the Newick tree format.
   http://evolution.genetics.washington.edu/phylip.html
  PHYLIP (Phylogeny Inference Package), by J. Felsenstein.
   http://paup.csit.fsu.edu/
  PAUP*, Phylogenetic Analysis Using Parsimony (*and Other Methods), by D.L. Swofford. Version 4. Sinauer Associates. Sunderland, Mass.
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