Core-genome analysis

A consensus core-genome was determined as the intersection of the clusters computed by the BDBH, COG-triangles and OMCL algorithms using the script compare_clusters.pl (option “-t <em>number of genomes</em>”) of GET_HOMOLOGUES software package. The resulting core-genome clusters were processed with the GET_PHYLOMARKERS software package. For core-genome-based phylogenetic analyses, the latter pipeline was run using both DNA and protein sequences, thus generating core-genome and core-proteome phylogenies, respectively. The protein alignment outputted by the cpAAI pipeline (see below) was also used as input for phylogenetic analysis. A ML phylogeny was inferred under the best-fitting substitution model by employing IQ-TREE Version 2.1.3 and ModelFinder (integrated in IQ-TREE), following the same approach as implemented in the GET_PHYLOMARKERS package.