bio-epidemiological-genomics-phylodynamics - Time-scaled phylogeny and evolutionary dynamics analysis
Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2
Tags
Updated: 2026-03-22Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Build time-scaled phylogenetic trees
- Estimate molecular clock rates
- Reconstruct ancestral sequences
- Analyze discrete traits
- Extract population size trajectories
- Prepare BEAST2 XML configuration
Inputs
- Genetic alignment
- Phylogenetic tree
- Sample dates
- Location states
- BEAST2 XML template
Outputs
- Time-scaled phylogenetic tree
- Ancestral sequences
- Molecular clock rate
- Coalescent skyline
- BEAST2 XML configuration
Requirements
- Python 3.x
- BioPython 1.83+
- TreeTime 0.11+
- BEAST2