option  	
--auto 		An appropriately strategy is automatically selected according to data size (Beta). default: off
--globalpair 	All pairwise alignments are computed with the FFT approximation. default: off
--localpair 	All pairwise alignments are computed by the Smith-Waterman algorithm. default: off
--memsave 	Memory saving. default: auto
--op n 		n = gap opening penalty for group-to-group alignment. n = 1.53 by default.
--ep n 		n = offset value, which works like gap extension penalty, for group-to-group alignment. n = 0.123 by default.
--lop n 	n = gap opening penalty for local alignment. n = -2 by default.
--lep n 	n = offset value, which works like gap extension penalty for local alignment. n = +0.1 by default.
--lexp n 	n = gap extension penalty for local alignment. n = -0.1 by default.
--bl n 		Scoring matrix = BLOSUM n, n = 30, 45, 62 (default), 80.
--jtt n 	Scoring matrix = JTT n PAM.
--nuc 		Sequence type = nucleotide. default: auto
--amino 	Sequence type = amino acid. default: auto
--retree n 	n is the number of tree re-buiding in progressive method. See the paper for details. n = 2 (default), 3, or so
--maxiterate n 	n is the maximum number of iterative refinement. default: 0
--fft 		FFT is enabled at progressive alignment stage. See the paper for details.
--nofft 	FFT is disabled.
--clustalout 	Output format: clustal format. default: fasta format
--reorder 	Output order: aligned. default: same as input order
--quiet 	Do not report progress.