DYNAMITE

DYNAMITE identifies dynamic transmission epicenters in rapidly spreading viral populations by performing branch-wise phylogenetic analysis to detect static and dynamic transmission clusters.

Key Features:

• Branch-Wise Analysis: Performs branch-wise searches on phylogenetic trees to detect partial clades and non-homogeneous transmission patterns instead of relying on clade-wise summary statistics.
• Dynamic Cluster Detection: Detects both static and dynamic transmission clusters to capture evolving epicenters within viral populations.
• Phylogenetic Input Support: Analyzes trees scaled in substitutions per site provided in Newick or Nexus format and incorporates node support values during analysis.
• Simulation Validation: Validated using simulated viral outbreaks with varying cluster types and dynamics.
• Implementation: Implemented in R.

Scientific Applications:

• Molecular epidemiology: Characterizes transmission subgroups and epicenters within rapidly evolving viral populations.
• Transmission inference: Identifies clades connected via direct transmission or differing risk factors.
• Public health guidance: Provides phylogenetically derived information to inform intervention and outbreak mitigation strategies.

Methodology:

Analyzes phylogenetic trees scaled in substitutions per site (Newick or Nexus formats with node support values) using a branch-wise search to detect transmission clusters that exhibit non-homogeneous behavior over time.