Despite its utility, phylogenetic analysis in epidemiology faces several challenges: 1. Data Quality: The accuracy of phylogenetic analysis depends on the quality and completeness of genetic data. 2. Computational Complexity: Building and interpreting phylogenetic trees can be computationally intensive. 3. Genetic Recombination: Recombination events can complicate the analysis by introducing genetic variations that do not follow a simple tree structure. 4. Sampling Bias: Uneven sampling of genetic sequences from different populations can lead to biased results.
