A Model of Indel Evolution by Finite-State, Continuous-Time Machines.

ABSTRACT: We introduce a systematic method of approximating finite-time transition probabilities for continuous-time insertion-deletion models on sequences. The method uses automata theory to describe the action of an infinitesimal evolutionary generator on a probability distribution over alignments, where both the generator and the alignment distribution can be represented by pair hidden Markov models (HMMs). In general, combining HMMs in this way induces a multiplication of their state spaces; to control this, we introduce a coarse-graining operation to keep the state space at a constant size. This leads naturally to ordinary differential equations for the evolution of the transition probabilities of the approximating pair HMM. The TKF91 model emerges as an exact solution to these equations for th

SUBMITTER: Holmes I 

PROVIDER: S-EPMC7768254 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature