Bayesian Phylogenetic Inference
MCMC sampling under an Epidemic Birth-Death model
Molecular Evolution
Pruning Algorithm
True β (Birth)
True δ (Death)
Sequence Length
Simulate Data
Prior β Mean
Prior δ Mean
Start MCMC
Stop
FBD Fixed Params
T (origin): 100
ρ (extant samp.): 1.0
ψ (fossil rate): 0.0
r (removal prob): 1.0
Simulated True Tree
Current Sampled Tree
RF dist: —
Tree Uncertainty (DensiTree)
0 trees
MCMC Status
Generation: 0
Acceptance rate: —
Log posterior: —
Current β: —
Current δ: —
Parameter Recovery
Param
True
Post. Mean
β
—
—
δ
—
—
T, ρ, ψ, r held fixed
Trace — β (Birth) & δ (Death)
Posterior — β (Birth)
Posterior — δ (Death)
Alignment (first 50 bp)