Table 4.

Accuracy values of several methods for the PREFAB tests

Method	Identity (%)					CPU time (s)
	0–20	20–40	40–70	70–100	All
G-INS-i	46.75	82.77	96.30	98.60	68.85	16 030
H-INS-i	48.22	83.32	95.83	98.64	69.70	15 060
F-INS-i	48.00	83.35	95.83	98.62	69.61	9007
H-INS-1	46.13a	82.16a	95.42b	98.60	68.27	9910
FFT-NS-i	45.72a	80.95a	93.83b	98.55	67.48	4176
FFT-NS-2	43.19a	79.52a	93.23b	98.47	65.74	930.4
FFT-NS-1	40.90a	77.50a	93.46a	98.59	63.92	666.2
TCoffee 2.02	45.30a	82.36b	95.20	98.62	67.96	973 600
PROBCONS 1.06	45.63b	82.10	95.01b	98.18	67.95	142 200
MUSCLE-i	42.77a	80.43a	95.43	98.28	66.05	13 260
MUSCLE-fast	38.44a	76.65a	93.42a	97.91	62.44	544.1
CLUSTAL W (default)	33.96a	74.14a	93.54b	97.85	59.45	12 970

The highest accuracy value within each percent identity range is in bold letters.

^aThe difference from the highest accuracy was found to be significant (P < 0.01) by both the Wilcoxon test and the Friedman test.

^bThe Wilcoxon test showed a significant difference but the Friedman test did not. See Table 1 for command-line options for each strategy in MAFFT. Options of other programs are as follows:

TCoffee, default;

PROBCONS, default;

MUSCLE-i, muscle -maxiters 1000;

MUSCLE-fast, muscle -sv -maxiters 1 -diags1 -distance1 kbit20_3;

CLUSTAL W (default), default.