bio-epidemiological-genomics-phylodynamics - Time-scaled phylogenies and evolutionary dynamics
Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis
Tags
Updated: 2026-03-22Capabilities
Typical Inputs
Typical Outputs
What this skill does
- construct time-scaled phylogenies
- estimate divergence times
- estimate molecular clock rates
- estimate ancestral states
- analyze population dynamics
- reconstruct ancestral sequences
- analyze discrete traits
Inputs
- genetic sequence alignment
- sample collection dates
- phylogenetic tree
- trait states metadata
Outputs
- time-calibrated phylogenetic tree
- molecular clock rate estimates
- ancestral state reconstructions
- skyline plot data
- coalescent skyline results
Requirements
- Python environment
- TreeTime 0.11+
- BioPython 1.83+