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Phylogenetic trees that are based on a specific sequence evolution model such as the Jukes-Cantor model can be estimated using maximum likelihood (Felsenstein 1981). This may require some approximations to make the inference computationally tractable.

ReferencesReference

– Felsenstein, J., 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, (17): 368–376.

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