STEM-hy: Species Tree Estimation using Maximum likelihood (with hybridization)

Version 1.0

Laura S. Kubatko and Travis Treseder
Department of Statistics
The Ohio State University
Columbus, OH 43210

Copyright 2007-2012 by Laura Salter Kubatko. This software is provided "as is" without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and documentation, is distributed free of charge.

The basic analyses incorporated in STEM-hy are described in the following publication:
Kubatko, L., B. C. Carstens, and L. L. Knowles. 2009. STEM: Species Tree Estimation
using Maximum likelihood for gene trees under coalescence, Bioinformatics, available here
(doi: 10.1093/bioinformatics/btp079).

The hybridization methods are described in the following publication:
Kubatko, LS. 2009. Identifying Hybridization Events in the Presence of Coalescence
via Model Selection, Systematic Biology 58(5): 478-488, available here.

About the Program

STEM-hy is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model. The program has the following functionality:


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Version History:

STEM-hy, Version 1.0, Released January 10, 2012.
Version 2.0, Released January 21, 2011.
Version 1.1, Released November 26, 2008.
Version 1.01 beta, Released February 2006.


Continued development of STEM/STEM-hy is based upon work supported by the National Science Foundation under Grants DMS 0104290, DMS 0702277, and DEB 0842219. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Contact Info

Questions or comments concerning the program can be e-mailed to me at Please also e-mail me if you'd like to be advised when updated versions of the program become available.

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