Table 2.

Comparison of Different Options Using the 16S.B.ALL Data Set (Mirarab et al. 2012).

Data	Method	Accuracy	CPU Time	Actual Timea
Case 1	mafft ––multipair ––addfragments frags existingmsa	0.9969	6.67 days	18.3 h
	mafft ––6merpair ––addfragments frags existingmsa	0.9949	3.76 h	36.2 min
	mafft ––localpair ––add  frags existingmsa	0.9707	23.4 daysb	2.43 daysb
	mafft ––6merpair ––add frags existingmsa	0.9604	1.32 h	1.44 h
	profile alignment	0.2779	15.5 h	1.60 h
Case 2	mafft ––6merpair ––addfragments frags existingmsa	0.9969	4.54 h	33.8 min
Case 3	mafft ––6merpair ––addfragments frags existingmsa	0.9949	1.79 days	5.91 h

Note.—The estimated alignments were compared with the CRW alignment to measure the accuracy (the number of correctly aligned letters/the number of aligned letters in the CRW alignment). Calculations were performed on a Linux PC with 2.67 GHz Intel Xeon E7-8837/256 GB RAM (for the case marked with superscript alphabet “b”), or on a Linux PC with 3.47 GHz Intel Xeon X5690/48 GB RAM (for the other cases). Case 1: 13,822 sequences in the existing alignment × 13,821 fragments; Case 2: 1,000 sequences in the existing alignment × 138,210 fragments; Case 3: 13,822 sequences in the existing alignment × 138,210 fragments.

^aWall-clock time with 10 cores. Command-line argument for parallel processing is ––thread 10.

^bFull command-line options are as follows: mafft ––localpair ––weighti 0 ––add frags existingmsa.