3.2. Phylogenetic Tree

The tree was constructed with 58 S. pyogenes ST62/emm87 genome sequences available in the GenBank and SRA. These sequences were aligned using ROARY (https://github.com/sanger-pathogens/Roary; accessed on 23 February 2023) and the command “roary -e --mafft -p 8 *.gff” for core genome alignment. The maximum likelihood tree was achieved by employing RaxMLGUI [43] with the GAMMA distribution and GTR substitution model and default parameters with 1000 bootstrap replicates. The tool “Interactive Tree of Life” (iTOL) v.4 was used for tree visualizations and editions [44].