Data from: Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST

Guy Baele, Mandev Gill, Paul Bastide, Philippe Lemey & Marc Suchard
Markov models of character substitution on phylogenies form the foundation of phylogenetic inference frameworks. Early models made the simplifying assumption that the substitution process is homogeneous over time and across sites in the molecular sequence alignment. While standard practice adopts extensions that accommodate heterogeneity of substitution rates across sites, heterogeneity in the process over time in a site-specific manner remains frequently overlooked. This is problematic, as evolutionary processes that act at the molecular level are...
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