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

Reference

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

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