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Bioinformatics Advance Access originally published online on May 12, 2008
Bioinformatics 2008 24(13):1540-1541; doi:10.1093/bioinformatics/btn230
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

André Wehe 1, Mukul S. Bansal 1, J. Gordon Burleigh 2 and Oliver Eulenstein 1,*

1Department of Computer Science, Iowa State University, Ames, IA 50011 and 2NESCent, Durham, NC 27705, USA

*To whom correspondence should be addressed.


  Abstract

Summary: DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++.

Availability: DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Contact: oeulenst{at}cs.iastate.edu

Associate Editor: Martin Bishop

Received on November 5, 2007; revised on May 7, 2008; accepted on May 8, 2008

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