Evolutionary Bioinformatics

Improved Heuristics for Minimum-Flip Supertree Construction

Submit a Paper

Evolutionary Bioinformatics 2006:2 347-356

Published on 28 Feb 2007

Further metadata provided in PDF

Sign up for email alerts to receive notifications of new articles published in Evolutionary Bioinformatics

Duhong Chen1, Oliver Eulenstein1, David Fernández-Baca1 and J.Gordon Burleigh2

1Department of Computer Science, Iowa State University, Ames, IA 50011, U.S.A. 2Section of Evolution and Ecology, University of California, Davis, CA 95616, U.S.A.; Current Address, NESCent, Durham, NC 27705, U.S.A.

Abstract: The utility of the matrix representation with flipping (MRF) supertree method has been limited by the speed of its heuristic algorithms. We describe a new heuristic algorithm for MRF supertree construction that improves upon the speed of the previous heuristic by a factor of n (the number of taxa in the supertree). This new heuristic makes MRF tractable for large-scale supertree analyses and allows the first comparisons of MRF with other supertree methods using large empirical data sets. Analyses of three published supertree data sets with between 267 to 571 taxa indicate that MRF supertrees are equally or more similar to the input trees on average than matrix representation with parsimony (MRP) and modified mincut supertrees. The results also show that large dif ferences may exist between MRF and MRP supertrees and demonstrate that the MRF supertree method is a practical and potentially more accurate alternative to the nearly ubiquitous MRP supertree method.




BibTex citation   (BIBDESK, LATEX)


What Your Colleagues Say About Evolutionary Bioinformatics
Having just published in a Libertas Academica journal (Evolutionary Bioinformatics) for the first time, I can attest that I was impressed by the process. Every stage from submission to typesetting and correspondence on matters relating to publishing was simple and efficient. In addition to this, regular updates of the status of the manuscript (with clear explanation of the status) enabled the process to be transparent and informative. I would not hesitate to use Libertas Academica ...
Dr Kevin Arbuckle (University of Liverpool, Merseyside, UK)
More Testimonials

Quick Links

New article and journal news notification services