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Found 3 papers, 2 papers with code
Random-effects substitution models for phylogenetics via scalable gradient approximations
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process.
Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis
Even in the presence of non-trivial phylogenetic model constraints, we show that one may analytically address latent factor uncertainty in a way that (a) aids model flexibility, (b) accelerates computation (by as much as 500-fold) and (c) decreases required tuning.
From viral evolution to spatial contagion: a biologically modulated Hawkes model
Mutations sometimes increase contagiousness for evolving pathogens.
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