Abstract: In this note, we characterize the embeddability of generic Kimura 3ST Markov matrices in terms of their eigenvalues. As a consequence, we are able to compute the volume of such matrices relative to the volume of all Markov matrices within the model. We also provide examples showing that, in general, mutation rates are not identifiable from substitution probabilities. These examples also illustrate that symmetries between mutation probabilities do not necessarily arise from symmetries between the corresponding mutation rates.
Recommendations
- Embeddability and rate identifiability of Kimura 2-parameter matrices
- The embedding problem for Markov matrices
- The model-specific Markov embedding problem for symmetric group-based models
- An open set of 4×4 embeddable matrices whose principal logarithm is not a Markov generator
- Embeddable Markov matrices
Cites work
- scientific article; zbMATH DE number 3138903 (Why is no real title available?)
- scientific article; zbMATH DE number 3943611 (Why is no real title available?)
- Embeddable Markov matrices
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Cited in
(8)- The model-specific Markov embedding problem for symmetric group-based models
- Embedding of Markov matrices for \(d \leqslant 4\)
- An open set of 4×4 embeddable matrices whose principal logarithm is not a Markov generator
- The embedding problem for Markov matrices
- Embeddability and rate identifiability of Kimura 2-parameter matrices
- Notes on Markov embedding
- Embeddability of centrosymmetric matrices capturing the double-helix structure in natural and synthetic DNA
- Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
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