… fit compared to the ones obtained in this section for the psaB and ndhD genes, as well as
the ability of state-of-the-art Bayesian model selection to select the generative substitution …

… These analyses of simulated data show that MMMs can easily be used in combination with
recent developments in Bayesian model selection, and provide additional support for our …

… Linear Models (GLM) ideas to Bayesian rate matrix … Model for Continuous Time Markov
Chains (GLM-CTMC) structured prior construction. In the motivating example of protein evolution, …

… countable state space S and evolving in continuous time [18]. A … The choice of MITL is justified
because time-bounded linear … use the binomial observation model in Bayes's theorem. In …

… In this study, we examine a general continuous-time Markov model of the evolution of an
entire sequence via insertions, deletions and substitutions. This model could be regarded as an …

… For example, in the protein evolution problem motivating the work in this paper, one could
tie … We select a specific set of features, described in Supplement 8, that match the degrees of …

… continuous time Markov models used to describe sequence … The above models consist of
continuous time Markov chains … The introduction of Bayesian integration techniques in TKF91 …

… 3.1, the moment closure method results in a system of ODEs that describe the evolution of …
within the continuous-time differential equations approach of [33], which dictates the choice of …

… probabilities of sequence alignments via evolutionary processes on an entire sequence. …
under a continuous-time Markov model, which describes the stochastic evolution of an entire …

… in a system of ODEs that describe the evolution of the expected values and the covariances
… the continuous-time differential equations approach of [33], which dictates the choice of …