A practical method for exact computation of subtree prune and regraft distance

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 article, 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 ef.ciency. Our experimental results indicate that our method can compute the exact rSPR distance for many large trees with large rSPR distance. © The Author 2008. Published by Oxford University Press. All rights reserved.