2.5. Clock rate analysis
The Delta and Omicron sequences were extracted based on the region shown
in the Supplementary Table 4. The datasets were aligned using MAFFT
v.7.5.0 using local pair algorithm. The sequences were filtered by
removing the redundant sequence and dropping all sequences containing
āNā. The clean datasets were used for clock rate analysis.
Clock rate analysis parameter was created using Beauti v.1.10.4and Bayesian analysis was performed using BEAST v1.10.4 .
HKY-Gamma substitution model and uncorrelated log-normal relaxed
molecular clock were set for the run. Priors were set to classic priors.
The chain length is 4 x 50 million with sampling every 50 thousand. Log
files were combined using LogCombiner v1.10.4. Run results were
evaluated using Tracer v1.7.1 . The ESS value higher than 100
shown acceptable quality run. Molecular Clock was observed from a report
generated by Tracer .