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Bioinformatics Advance Access published online on November 19, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn606
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A Practical Method for Exact Computation of Subtree Prune and Regraft Distance

Yufeng Wu

Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, U.S.A.

To whom correspondence should be addressed. De. Yufeng Wu, E-mail: ywu{at}engr.uconn.edu


  Abstract

Motivation: Subtree prune and regraft (SPR) is one kind of tree rearrangements that has seen applications in solving several computational biology problems. The minimum number of rooted SPR (rSPR) operations needed to transform one rooted binary tree to another is called the rSPR distance between the two trees. Computing the rSPR distance has been actively studied in recent years. Currently, there is a lack of practical software tools for computing the rSPR distance for relatively large trees with large rSPR distance.

Results: In this paper, we present a simple and practical method that computes the exact rSPR distance with integer linear programming. By applying this new method on several simulated and real biological datasets, we show that our new method outperforms existing software tools in term of accuracy and efficiency. Our experimental results indicate that our method can compute the exact rSPR distance for many large trees with large rSPR distance.

Availability: A software tool, SPRDist, is available for download from the web page: http://www.engr.uconn.edu/~ywu.

Contact: ywu{at}engr.uconn.edu

Associate Editor: Prof. Martin Bishop

Received on September 26, 2008; revised on November 17, 2008; accepted on November 17, 2008

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