© 2005 Society of Systematic Biologists
Analysis and Visualization of Tree Space
1 Section of Integrative Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin Austin, Texas, 78712, USA E-mail: dhillis{at}mail.utexas.edu (D.M.H.)
2 Department of Mathematics and Computer Science, Lehman College–City University of New York Bronx, New York, 10468, USA E-mail: stjohn{at}lehman.cuny.edu
Edited by Frank Anderson: Associate Editor
 |
Abstract |
|---|
We explored the use of multidimensional scaling (MDS) of tree-to-tree pairwise distances to visualize the relationships among sets of phylogenetic trees. We found the technique to be useful for exploring "tree islands" (sets of topologically related trees among larger sets of near-optimal trees), for comparing sets of trees obtained from bootstrapping and Bayesian sampling, for comparing trees obtained from the analysis of several different genes, and for comparing multiple Bayesian analyses. The technique was also useful as a teaching aid for illustrating the progress of a Bayesian analysis and as an exploratory tool for examining large sets of phylogenetic trees. We also identified some limitations to the method, including distortions of the multidimensional tree space into two dimensions through the MDS technique, and the definition of the MDS-defined space based on a limited sample of trees. Nonetheless, the technique is a useful approach for the analysis of large sets of phylogenetic trees.
Keywords: Bayesian analysis; multidimensional scaling; phylogenetic analysis; tree space; visualization
Received May 23, 2004; Revised August 3, 2004; Accepted August 26, 2004
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Stamatakis, P. Hoover, and J. Rougemont A Rapid Bootstrap Algorithm for the RAxML Web Servers Syst Biol, October 1, 2008; 57(5): 758 - 771. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. M. W. Nye Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies Syst Biol, October 1, 2008; 57(5): 785 - 794. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Lakner, P. van der Mark, J. P. Huelsenbeck, B. Larget, and F. Ronquist Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics Syst Biol, February 1, 2008; 57(1): 86 - 103. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Morrison Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences Syst Biol, December 1, 2007; 56(6): 988 - 1010. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Soria-Carrasco, G. Talavera, J. Igea, and J. Castresana The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees Bioinformatics, November 1, 2007; 23(21): 2954 - 2956. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. B. Smythe, M. J. Sanderson, and S. A. Nadler Nematode Small Subunit Phylogeny Correlates with Alignment Parameters Syst Biol, December 1, 2006; 55(6): 972 - 992. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. A. Matsen A Geometric Approach to Tree Shape Statistics Syst Biol, August 1, 2006; 55(4): 652 - 661. [Abstract] [Full Text] [PDF]
|
|