Phylodynamic simulations in Julia


I am trying to figure out the best way to perform phylodynamic simulations in Julia. I’ve come across the Gillespie.jl, Biosimulation.jl and the ModellingToolKit.jl packages. Great talk for ModelingToolKit.jl by the way at juliacon 2021.

I’m not sure how to get started on this topic. Which package is the best starting point for Phylodynamics? Are there any good examples on the web?

Catalyst is by far the most active community in this bio modeling domain, and it uses ModelingToolkit.jl under the hood but gives it a reaction-based DSL. I don’t think I’ve written any tutorials with it that do phylodynamic simulations but the tutorials in there should be “rather close”, and if anything is missing I’d be happy to help you out on the Discourse and add the answers as new tutorials (that’s how things improve of course!).

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