SSA A program for inferring maximum likelihood phylogenies from DNA sequences
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molecular sequence DNA sequence DNA molecular analysis hierarchical likelihood edit DNA sequences DNA sequences editor DNA sequences analysis analyze DNA sequences aligned DNA sequences DNA sequences simulate phylogenies phylogenies simulation estimate large phylogenies large phylogenies estimation large phylogenies analysis molecular clock maximum likelihood allele

SSA Description

SSA was developed to be 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.

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