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Bioinformatics Advance Access published online on February 10, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp079
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

STEM: Species Tree Estimation using Maximum likelihood for gene trees under coalescence

Laura S. Kubatko 1,*, Bryan C. Carstens 2 and L. Lacey Knowles 3

1Departments of Statistics and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210
2Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
3Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109

*To whom correspondence should be addressed. Dr. Laura Kubatko, E-mail: lkubatko{at}stat.osu.edu


  Abstract

Summary: STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood, and compute ML branch lengths for a user-input species tree.

Availability: The STEM package, including source code, is freely available at http://www.stat.osu.edu/~lkubatko/software/STEM/.

Contact: lkubatko{at}stat.osu.edu

Supplemental Information: Available on the Bioinformatics web site.

Associate Editor: Prof. Martin Bishop

Received on November 28, 2008; revised on February 4, 2009; accepted on February 4, 2009

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