/usr/local/bin/mafft: Cannot open -help.
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  MAFFT v6.935b (2012/08/21)
  http://mafft.cbrc.jp/alignment/software/
  NAR 30:3059-3066 (2002), Briefings in Bioinformatics 9:286-298 (2008)
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High speed:
  % mafft in > out
  % mafft --retree 1 in > out (fast)

High accuracy (for <~200 sequences x <~2,000 aa/nt):
  % mafft --maxiterate 1000 --localpair  in > out (% linsi in > out is also ok)
  % mafft --maxiterate 1000 --genafpair  in > out (% einsi in > out)
  % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)

If unsure which option to use:
  % mafft --auto in > out

--op # :         Gap opening penalty, default: 1.53
--ep # :         Offset (works like gap extension penalty), default: 0.0
--maxiterate # : Maximum number of iterative refinement, default: 0
--clustalout :   Output: clustal format, default: fasta
--reorder :      Outorder: aligned, default: input order
--quiet :        Do not report progress
--thread # :     Number of threads (if unsure, --thread -1)