Embeddability and rate identifiability of Kimura 2-parameter matrices
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Publication:2299271
Abstract: Deciding whether a Markov matrix is embeddable (i.e. can be written as the exponential of a rate matrix) is an open problem even for matrices. We study the embedding problem and rate identifiability for the K80 model of nucleotide substitution. For these matrices, we fully characterize the set of embeddable K80 Markov matrices and the set of embeddable matrices for which rates are identifiable. In particular, we describe an open subset of embeddable matrices with non-identifiable rates. This set contains matrices with positive eigenvalues and also diagonal largest in column matrices, which might lead to consequences in parameter estimation in phylogenetics. Finally, we compute the relative volumes of embeddable K80 matrices and of embeddable matrices with identifiable rates. This study concludes the embedding problem for the more general model K81 and its submodels, which had been initiated by the last two authors in a separate work.
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Cited in
(10)- The embedding problem for Markov matrices
- The model-specific Markov embedding problem for symmetric group-based models
- Embedding of Markov matrices for \(d \leqslant 4\)
- Markov evolution algebras
- An open set of 4×4 embeddable matrices whose principal logarithm is not a Markov generator
- Embeddability of Kimura 3ST Markov matrices
- On monotone Markov chains and properties of monotone matrix roots
- On equal-input and monotone Markov matrices
- Accessible Maps in a Group of Classical or Quantum Channels
- Embeddability of centrosymmetric matrices capturing the double-helix structure in natural and synthetic DNA
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