Embeddability and rate identifiability of Kimura 2-parameter matrices

DOI10.1007/S00285-019-01446-0zbMATH Open1431.60074arXiv1902.08555OpenAlexW2988434190WikidataQ91199952 ScholiaQ91199952MaRDI QIDQ2299271FDOQ2299271

Marta Casanellas, Jordi Roca-Lacostena, Jesús Fernández-Sánchez

Publication date: 21 February 2020

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

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 $4imes4$ matrices. We study the embedding problem and rate identifiability for the K80 model of nucleotide substitution. For these $4imes4$ 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.

Full work available at URL: https://arxiv.org/abs/1902.08555

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• Embeddability of Kimura 3ST Markov matrices
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zbMATH Keywords

Markov matrixMarkov generatorembedding problemmatrix logarithmnucleotide substitution modelrate identifiability

Mathematics Subject Classification ID

Problems related to evolution (92D15) Markov chains (discrete-time Markov processes on discrete state spaces) (60J10) Matrix exponential and similar functions of matrices (15A16) Stochastic matrices (15B51) Continuous-time Markov processes on discrete state spaces (60J27)

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Cited In (9)

• Embedding of Markov matrices for \(d \leqslant 4\)
• The model-specific Markov embedding problem for symmetric group-based models
• Markov evolution algebras
• An open set of 4×4 embeddable matrices whose principal logarithm is not a Markov generator
• 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
• The embedding problem for Markov matrices

Uses Software

• mftoolbox

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