A package for inferring and viewing transmission clusters from sequence alignments and sample dates.
Related publications:
- Stimson, J., Gardy, J., Mathema, B., Crudu, V., Cohen, T., & Colijn, C. (2019). Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Molecular Biology and Evolution, 36(3), 587–603. https://doi.org/10.1093/molbev/msy242