2.4 Recombination analysis
In order to find potential natural genetic recombination events in the
evolution of the Vietnamese CPV-2 strains, the dataset of CPV-2 genomes
used in the evolutionary analysis (section 2.3) were further subjected
to recombination analysis using various statistical methods, including
recombination detection program (RDP), GENECONV, BootScan, MaxChi,
Chimaera, SiScan, and 3Seq with the default settings in the RDP package
version 4.0 (Piewbang et al., 2018). Because many recombination signals
would be detected during the test run and the different algorithms might
be inconsistent, then the acceptance criteria of any potential
breakpoint signal must be revealed by at least four methods withp -values < 0.01 was applied to recognize any
potentially positive recombination event.