SSA 1.0 – Inference of Maximum Likelihood Phylogenetic Trees Using a Stochastic Search Algorithm

SSA 1.0


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.


Laura S. Kubatko




  • Linux/ Windows





Salter, L. and D. Pearl. 2001.
Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees,
Systematic Biology 50(1): 7-17.

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