bio-epidemiological-genomics-phylodynamics - Build time-scaled phylogenies for outbreak analysis
Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime for outbreak analysis
Tags
Updated: 2026-03-22Capabilities
Typical Inputs
Typical Outputs
What this skill does
- load Newick tree
- load alignment file
- load dates file
- run molecular clock analysis
- estimate divergence times
- estimate clock rate
- estimate root date
- reconstruct ancestral sequences
- analyze discrete traits
- extract skyline plot
- interpret clock results
Inputs
- Newick tree file
- alignment file
- dates file
- metadata file
- states file
Outputs
- time-scaled tree
- clock rate estimate
- divergence time estimate
- ancestral sequences
- skyline plot
- mugration analysis results
Requirements
- Python environment
- BioPython 1.83+
- TreeTime 0.11+
- scanpy 1.10+