bio-epidemiological-genomics-transmission-inference - Infer pathogen transmission networks and transmission pairs
Infer pathogen transmission networks and estimate who-infected-whom from genomic and epidemiological data using TransPhylo and distance-based algorithms.
Tags
Updated: 2026-09-18Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Infer transmission trees using TransPhylo
- Prepare input data for TransPhylo
- Extract consensus transmission tree
- Estimate basic reproduction number
- Identify superspreaders in outbreak
- Infer transmission pairs from distance
- Plot transmission network graph
Inputs
- Dated phylogeny Nexus file
- Sample collection dates
- Genomic distance matrix
Outputs
- Consensus transmission tree
- Transmission pairs data table
- Basic reproduction number R0 estimate
- Superspreaders list
- Transmission network graph figure
Requirements
- R environment with TransPhylo and ape
- Python environment with BioPython, pandas, numpy, networkx, matplotlib