Fit birth-death model to real data

[ArtPoon]

Current parameter settings for simulating birth-death trees are basically arbitrary. Either:

• justify these specific values;
• evaluate a range of values (increases replicates combinatorially)
• fit BD model to actual data sets to see what values are "realistic"

[ArtPoon]

• Use BEAST2 and phylodynamics module (installed with BEAST package manager).
• Select serial birth-death model (same as BD model in TreeSim)
• Fit this model to actual HIV RNA data set (alignment) that has sufficient number of sequences, genetic diversity (signal) and number of time points.
• Take posterior estimates from BEAST2 as parameter settings for simulating BD trees with TreeSim.