bio-epidemiological-genomics-phylodynamics - Time-scaled Phylogeny and Evolutionary Dynamics Analysis
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
- build time-scaled trees
- estimate clock rates
- estimate divergence times
- reconstruct ancestral sequences
- analyze population dynamics
- prepare date files
- prepare BEAST2 configuration
Inputs
- sequence alignment file
- phylogenetic tree file
- sample dates file
- states file
Outputs
- time-scaled phylogenetic tree
- molecular clock rate
- ancestral sequences
- population dynamics data
Requirements
- Python environment
- TreeTime 0.11+
- BioPython 1.83+
- scanpy 1.10+
- BEAST2