To infer recombination events in bacterial genomes, we used the maximum likelihood implementation of ClonalFrame, ClonalFrameML. MAGs (only high quality) were aligned with progressiveMauve, which is p
Pantagruel (Lassalle et al., 2019) was used to infer a maximum-likelihood (ML) “core genome tree” from the concatenated alignments of 291 core-genome genes extracted from the 889 assembled V
