Table 4.

Computational time for each phylogenetic analysis

Sequence type	PhyML3 (bootstrapping)	PhyML3 (aLRT)	BEAST ver.1.7
Whole genome	34h59min55sec	2min49sec	21h40min45sec
Consensus sequence	4h50min9sec	1min24sec	1h47min24sec
H37Rv	19h24min38sec	2min37sec	2h38min31sec

For PhyML, two tree selection methods, 100 bootstrappings and aLRT were performed. In the bootstrap analyses, multithreading with 16 CPUs were utilized to reduce the computational time. For BEAST, 10 million samplings were performed for each analysis. Computational times were based on the log file of each analysis.