Generating Markov evolutionary matrices for a given branch length

DOI10.1016/J.LAA.2012.11.009MaRDI QIDQ1938705zbMATH OpenOpenAlexWikidataFDO

Authors Anna M. Kedzierska, Marta Casanellas

Publication date 22 February 2013

Published in Linear Algebra and its Applications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1112.3529

zbMATH Keywords

algorithmdeterminantstochastic matricesMarkov matrixbranch lengthdiscrete-time modelevolutionary modelnonhomogeneous evolutionary processes

Mathematics Subject Classification ID

Markov chains (discrete-time Markov processes on discrete state spaces) (60J10) Determinants, permanents, traces, other special matrix functions (15A15) Stochastic matrices (15B51)

Abstract: Under a markovian evolutionary process, the expected number of substitutions per site (also called branch length) that have occurred when a sequence has evolved from another according to a transition matrix $P$ can be approximated by $-1/4logdetP.$ When the Markov process is assumed to be continuous in time, i.e. $P=expQt$ it is easy to simulate this evolutionary process for a given branch length (this amounts to requiring $Q$ of a certain trace). For the more general case (what we call discrete-time models), it is not trivial to generate a substitution matrix $P$ of given determinant (i.e. corresponding to a process of given branch length). In this paper we solve this problem for the most well-known discrete-time models JC*, K80*, K81*, SSM and GMM. These models lie in the class of nonhomogeneous evolutionary models. For any of these models we provide concise algorithms to generate matrices $P$ of given determinant. Moreover, in the first four models, our results prove that any of these matrices can be generated in this way. Our techniques are mainly based on algebraic tools.

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Cites work

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Cited in

(7)

• Markov evolution algebras
• An open set of 4×4 embeddable matrices whose principal logarithm is not a Markov generator
• Generating embeddable matrices whose principal logarithm is not a Markov generator
• Closed form modeling of evolutionary rates by exponential Brownian functionals
• A unified approach to the transition matrices of DNA substitution models
• Counting labeled transitions in continuous-time Markov models of evolution
• Embeddability of centrosymmetric matrices capturing the double-helix structure in natural and synthetic DNA

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