BEAST XML files accompanying the manuscript 'Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework' by Guy Baele, Mandev S. Gill, Philippe Lemey, and Marc A. Suchard
The data sets analysed are the following:
- Ebola data set from Dudas et al., 2017, subset by Hill and Baele, 2019
- Rabies data set from Biek et al., 2007
- Rice yellow mottle virus (RYMV) data set from Trovao et al., 2015
Files marked fixed assume a provided or user-defined tree topology, whereas files marked variable estimate the tree topology during the analysis. Files marked BUMCMC employ a block-update Markov chain Monte Carlo transition kernel developed by Gill et al., 2013, whereas files marked HMC employ the Hamiltonian Monte Carlo transition kernel discussed in our manuscript.