Ca. T. endolucinida core gene nucleotide alignment to infer recombination to mutation ratio

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 part of the Mauve genome alignment package version 2.0. Core genes; i.e., nucleotide sequences that were shared among all MAGs within a group, were extracted with a custom script, stripSubsetLCBs, which can be downloaded here. These core genes were then re-aligned with MUSCLE and cleaned with trimAl with the following parameters: -resoverlap 0.75 -seqoverlap 80.