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Visualizing Phylogenetic Trees Using TreeView
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 6.2
DOI:
10.1002/0471250953.bi0602s01
Online Posting Date:
January, 2003 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*.
Table of Contents
- Unit Introduction
- 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
- Bibliography
- Figures
- Tables
Figures
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Figure 6.2.1A Newick tree description. This tree is displayed graphically in Figure -
Figure 6.2.2A tree window in TreeView displaying a phylogenetic tree as a phylogram. The scale bar represents 0.1 substitutions per nucleotide site. The toolbar buttons enable the user to change the style in which the tree is drawn, toggle on and off the display of internal node labels, and print the tree. The screenshot shows TreeView running under MacOS; the Windows version is almost identical in appearance. -
Figure 6.2.3Using the Define Outgroup dialog box to specify an outgroup. In this example the species Lemur catta is selected in the ingroup list. Double clicking the selected item, or clicking on the “>>” button will move Lemur catta to the outgroup list. -
Figure 6.2.4The Print preview window in TreeView. In this example a large tree is being printed over three pages. -
Figure 6.2.5The Print Trees dialog in TreeView. The Layout dialog box specifies how many trees are drawn per page, and the order in which they are drawn. Other options that can be set are the fonts used for the leaf and internal labels, tree style, branch width, and tree order. -
Figure 6.2.6PAUP* dialog box displaying options that affect how trees are saved. To save bootstrap values in a format that TreeView can display, the value of Maximum number of decimal is set to 0, the Include Bootstrap/Jackknife Proportions checkbox is checked, and the As Internal Node Labels option is selected. -
Figure 6.2.7The same tree drawn in the four different styles available in TreeView. -
Figure 6.2.8Syntax diagram for the Newick Standard for describing phylogenetic trees. The names in rectangular boxes stand for elements of the tree description, such as the name of a leaf in the tree; punctuation in circular boxes are required parts of the format. Any path through the diagram that begins at the left and ends with an arrow on the right is a valid path. Alternative paths are often possible; for example, a descendant list may or may not have an associated internal node label and a branch length. -
Figure 6.2.9Three trees and their corresponding Newick tree descriptions. The top tree description specifies the topology of the tree, the middle specifies the same tree but with the addition of branch lengths, and the bottom description adds internal node labels. -
Figure 6.2.10An unrooted tree (A) and two rooted trees (B,C) that are consistent with that unrooted tree. -
Figure 6.2.11An example of the order in which nodes in a tree are visited when writing a Newick tree description.
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 | |
| 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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