Bayesian phylogenetic inference accounting for recombination in whole bacterial genomes

ClonalFrame2 infers bacterial phylogenies from whole genomes while accounting for recombination, recovering recombination parameters across 100 simulated datasets of 100 genomes each.

• Why it matters: Ignoring recombination can distort bacterial trees and undermine downstream analyses like dating, motivating a Bayesian approach that models both mutation and recombination.
• What they did: The method uses a hidden Markov model to integrate out recombination locations and targets the clonal genealogy plus three recombination parameters, with ancestral sequences recomputed during topology updates.
• The result: In simulations, recombination-aware trees were many times more accurate than those ignoring recombination, and in Staphylococcus aureus ST239 it produced a stronger temporal signal and more robust dated phylogeny.

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