2.5. Sequence, phylogenetic, and recombination analyses
The homologies of the nucleotide and deduced amino acid (aa) sequences
were determined using the MegAlign program in DNASTAR 7.0 software, and
a heat map was constructed based on sequence homology using HemI
software (Heatmap Illustrator, version 1.0.3.7); MEGA X 10.2.4
(https://www.megasoftware.net/) was used for multiple sequence alignment
and to subsequently build neighbor-joining phylogenetic trees with
bootstrap testing (1,000 replicates). Phylogenetic trees were pruned and
re-rooted using the Interactive Tree Of Life software, version 5.6.3
(https://itol.embl.de/), an online tool for displaying the circular tree
annotation. Recombination events were assessed using the recombination
detection program RDP 4.0 (version 4.9.5) with the RDP, GeneConv,
Chimaera, MaxChi, BootScan, SiScan, and 3Seq methods. The results were
used for Simi larity Plotting analysis using the SimPlot program version
3.5.1 with a window size of 200 bp and a step size of 20 bp.