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 Felsensteins 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.

The license of this software is Freeware, you can free download and free use this calculator software.