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

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.


Documentation only (pdf format)

SSA program for Sun/Sparc (executable, example, and documentation)

SSA program for AIX (executable, example, and documentation)

SSA program for Linux (executable, example, and documentation)

SSA program for PC's (executable, example, and documentation)

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.


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 Please also e-mail me if you'd like to be advised when updated versions of the program become available.

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