cbrc
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Supported in versions ≥6.8

Multithreading

% mafft --thread -1 input > output
% mafft --thread n input > output
% mafft --thread n --globalpair (other options) input > output

Separately specifying the number of threads for each calculation stage  Updated (2017/Jul)

% mafft --thread n --threadtb m --threadit p --globalpair (other options) input > output
  1. For all-to-all pairwise comparison, the number of threads specified with the --thread option are used.  The wall-clock time for this stage linearly decreases with the number of threads.
  2. For progressive alignment stage, the efficiency is not high (requiring large RAM) when using a large number (>>20) of threads. 
  3. For progressive alignment stage, too, the efficiency is not high when using a large number (>>20) of threads.  The number of threads in this stage is automatically restricted to 10 but can be increased or decreased by --threadit.