SSA: Inference of Maximum Likelihood Phylogenetic
Trees using a Stochastic Search Algorithm
Version 1.0
Laura Salter Kubatko
Department of Statistics
The Ohio State University
Columbus, OH 43210 lkubatko@stat.ohio-state.edu
Copyright 2002 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.
If you use this program in a publication, please
cite the following reference:
Salter, L.A. and D.K. Pearl (2001) Stochastic Search
Strategy for Estimation of Maximum Likelihood Phylogenetic Trees.
Systematic Biology 50(1): 7-17.
About the Program
SSA is a program for inferring maximum likelihood
phylogenies from DNA sequences. Two versions of the program are
available: one which assumes a molecular clock and one which does
not make this assumption. The method for searching the space of
trees for the ML tree is based on a simulated-annealing type
algorithm and is described in the reference above. The program
implements Felsenstein's F84 model of nucleotide substitution
and associated sub-models. The program
estimates the ML tree and branch lengths, and can optionally
estimate the transversion/transversion ratio. Upon termination,
the program returns the k trees of highest likelihood found
during the search, where k can be set by the user.
Source code: I am happy to provide the source code for the program to anyone who has
the book Numerical Recipes in C by Press et al. (and thus permission to use source code derived from it). Please e-mail me with your requests.
Acknowledgements
Continued development of SSA is based upon work supported by the National Science Foundation under Grant No. 0104290. 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.