Rainbow: A Toolbox for Phylogenetic Supertree Construction and Analysis
D. Chen, O. Eulenstein, and D. Fernández-Baca
Department of Computer Science
Iowa State University
Ames, IA 50011, USA
ABSTRACT
Summary: Rainbow is a program that provides a graphic user interface (GUI) to construct supertrees
using different methods. It also provides tools to analyze the quality of the supertrees produced.
Rainbow is available for Mac OS X, Windows and Linux.
Availability: Rainbow is free open-source software. Its binary files, source code, and manual and can
be downloaded from the Rainbow webpage: http://genome.cs.iastate.edu/Rainbow/.
Contact: duhong@iastate.edu
Phylogenetic supertrees are typically rooted evolutionary trees assembled from smaller rooted trees
that share some but not necessarily all taxa (leaf nodes) in common. Supertrees can make novel
statements about relationships among taxa that do not co-occur on any single source tree, while
retaining hierarchical information from the source trees. As a method of combining existing
phylogenetic information to produce more inclusive phylogenies, the supertree approach can
potentially resolve problems associated with other methods, such as absence of homologous characters,
incompatible data types, or non-overlapping sets of taxa (Sanderson et al., 1998, Bininda-Emonds et
al., 2002).
Supertree construction methods can be classified as either matrix-based or not. Examples of the
latter include most consensus supertree methods, MinCut (MC) algorithm (Semple and Steel, 2000),
and Modified MinCut (MMC) algorithm (Page, 2002). Matrix-based supertree methods encode the
source trees as a matrix that is then combined and analyzed using an optimization criterion. Two
examples of this approach are Matrix Representation with Parsimony (MRP) (Baum, 1992; Ragan,
1992) and Matrix Representation with Flipping (MRF) (Chen et al., 2003; Eulenstein et al., 2004).
Supertree programs available on the Internet include Thorely et al.’s RadCon (Thorely et al. 2000),
Salamin's SuperTree 0.85b (Salamin, 2002) and Page’s supertree0.3 (Page, 2003a). The first two
compute MRP matrices from phylogenetic trees, but do not integrate parsimony analyses on the output
matrices. Page’s program is a console application to construct MC and MMC supertrees.
Rainbow is a supertree analysis tool for Mac OS X, Windows and Linux that integrates graphic
tree display, supertree construction, and result analysis. Rainbow uses the NCL C++ library (Lewis,
2003) to interpret tree files in Nexus format (Maddison et al., 1997), and the TreeLib C++ class library
(Page, 2003b) for displaying trees. It can construct MRF/P, and MMC supertrees. The MRP and
MMC supertree implementations require the following programs: PAUP*4 (Swofford, 2002), which is
used for parsimony analyses, and Page’s supertree-0.3 program, which is needed to obtain MMC
supertrees. Rainbow determines the accuracy of constructed supertrees by how well they fit their
source trees. The fit is measured by the size of the normalized maximal agreement subtree (Eulenstein
et al., 2004), the symmetric difference, and the triplet fit (Page 2002).
Figure 1. A screen-shot of Rainbow under Mac OS X. Right frame: The tree navigation bar, showing
the currently open files. Bottom right frame: A source tree whose weight is being set. Top center:
The supertree wizard. Left frame: One of the resulting supertrees. Partially hidden from view are the
log and report windows (bottom left and center, respectively).
Figure 1 is a screen-shot of a typical Rainbow session. A supertree wizard guides the user in
setting parameters for the various supertree methods, such as the number of random-addition-sequence
replications to be performed, the maximum number of tie trees to be kept, and, for the MRF/P
heuristics, the branch swapping methods to be applied. It also provides a dialog box to set weights for
the source trees, so the user can construct weighted MRF/P, and weighted MMC supertrees. A log
window reports the progress of a supertree construction and a report window displays the accuracy
analysis of the constructed supertrees.
A Rainbow manual including hands-on examples is available through the Rainbow webpage.
Future plans include the integration of Quartet Suite 1.0 (Piaggio-Talice, 2004), that is an
implementation of a quartet-based supertree method by Piaggio-Talice et al. (2004).
ACKNOWLEDGMENTS
Rod Page generously provided his programs for calculating MMC supertrees and TreeLib library for
handling phylogenetic trees. J.G. Burleigh and Mike Sanderson tested the software and offered many
helpful suggestions. This work was supported in part by NSF grants 1053164 (Eulenstein), CCR9988348 (Fernández-Baca), and EF-0334832 (Eulenstein, Fernández-Baca).
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