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Dellicour 2020 Phylodynamic Workflow Rapidly

Dellicour et al. (2020) A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages

Workflow

1. Estimate a Maximum Likelihood Tree (IQTREE)
2. Rescale branch lengths to units of time (treetime, lsd)
3. Perform continuous phylogeography with BEAST on bivariate trait (latitude, longitude)

Progress

1. Successfully ran the tutorial.
2. Had mixed success with my own data.

Issues

1. Dataset is too large.
   • Maximize geographic diversity
   • Maximum temporal diversity.
2. For the full tree, the clock model needs to be set extremely small (1e-100) to initialize.
3. For certain subtrees, the clock model is correct.

It might be worth running BEAST 1.10

On the full dataset.