bio-epidemiological-genomics-phylodynamics - Time-scaled phylogenies for outbreak analysis
Construct time-scaled phylogenies and infer evolutionary dynamics
Tags
Updated: 2026-03-22Capabilities
Typical Inputs
Typical Outputs
What this skill does
- build time-scaled tree
- estimate divergence times
- estimate molecular clock rates
- reconstruct ancestral states
- analyze population dynamics
- interpret clock results
- prepare BEAST2 XML
Inputs
- sequence alignment
- phylogenetic tree
- sampling dates
- metadata file
Outputs
- time-scaled phylogeny
- divergence times
- molecular clock rates
- ancestral states
- population size trajectory
Requirements
- Python environment
- BioPython 1.83+
- TreeTime 0.11+
- scanpy 1.10+