Parallel algorithms for phylogenetic inference under a structured coalescent approximation.

ABSTRACT: While advances in molecular epidemiology and computational modeling have enhanced our capacity to track pathogen evolution, the accurate reconstruction of spatiotemporal transmission dynamics remains essential for developing epidemic preparedness frameworks and implementing outbreak response measures. Structured coalescent models offer a phylogeographic framework by restricting lineage coalescence events to geographically proximate host populations. Although the Bayesian structured coalescent approximation (BASTA) provides a tractable approach, contemporary phylogeographic analyses involving dozens of geographic localities and hundreds to thousands of viral genomes substantially exceed the computational capacity of existing implementations. The BASTA likelihood scales cubically with deme c

SUBMITTER: Shao Y 

PROVIDER: S-EPMC12485945 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature