Analysis and visualization of tree space.
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.
Hillis
David M
DM
Section of Integrative Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA. dhillis@mail.utexas.edu
Heath
Tracy A
TA
St John
Katherine
K
D001499:Bayes Theorem; D002965:Classification / Q000379:methods*; D003627:Data Interpretation, Statistical; D010802:Phylogeny; D012984:Software