MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

Supported in versions ≥6.9

Updated in version 7.297 (2016/Jun)

Direction of nucleotide sequences

Two options generate reverse complement sequences, as necessary, and align them together with the remaining sequences.
% mafft --adjustdirection input > output
is based on 6 mer counting and faster.

% mafft --adjustdirectionaccurately input > output
is based on DP and slower.

Update in version 7.297 (2016/Jun)

There is no change in usage.  Speed has been improved for large data.  There may be further changes in parameters and algorithm after several tests.