Skip Navigation


Bioinformatics Advance Access originally published online on November 19, 2008
Bioinformatics 2009 25(2):190-196; doi:10.1093/bioinformatics/btn606
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
25/2/190    most recent
btn606v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Wu, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wu, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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, USA


  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.

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

Contact: ywu{at}engr.uconn.edu

Associate Editor: Martin Bishop

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.