STEM: Species Tree Estimation using Maximum likelihood
Version 1.1
Laura Salter Kubatko
Department of Statistics
The Ohio State University
Columbus, OH 43210
lkubatko@stat.ohio-state.edu
Copyright 2007, 2008, 2009 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.
STEM is 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).
About the Program
STEM is a program for inferring maximum likelihood
species trees from a collection of estimated gene trees under the
coalescent model. The program will either return the exact ML tree,
compute the likelihood for a user-specified tree, or search for a set
of highest likelihood trees.
The method for searching the space of trees
is a simulated annealing
algorithm.
Downloads:
New - Google Users Group
Click
here
Version History:
Version 1.1, Released November 26, 2008.
- Improved input and output format.
- Allows for different taxon samples in each gene, thereby
enabling analysis when data are missing for some lineages for
some genes.
Version 1.01 beta, Released February 2006.
Acknowledgements
Continued development of STEM is based upon work supported by the National Science Foundation under Grant No. 0702277. 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 lkubatko@stat.ohio-state.edu. Please also e-mail me if you'd like to be advised when updated versions of the program become available.
Back to Laura's homepage