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The identifiability of tree topology for phylogenetic models, including covarion and mixture models

, : The identifiability of tree topology for phylogenetic models, including covarion and mixture models. Journal of Computational Biology 13(5): 1101-1113

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter. We establish tree identifiability for a number of phylogenetic models, including a covarion model and a variety of mixture models with a limited number of classes. The proof is based on the introduction of a more general model, allowing more states at internal nodes of the tree than at leaves, and the study of the algebraic variety formed by the joint distributions to which it gives rise. Tree identifiability is first established for this general model through the use of certain phylogenetic invariants.


PMID: 16796553

DOI: 10.1089/cmb.2006.13.1101

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