Journal
JOURNAL OF COMPUTATIONAL BIOLOGY
Volume 13, Issue 5, Pages 1101-1113Publisher
MARY ANN LIEBERT, INC
DOI: 10.1089/cmb.2006.13.1101
Keywords
phylogenetics; tree identifiability; covarion model; mixture model; rate variation; phylogenetic invariants
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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.
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