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.
The former works well in most cases, unless the sequences are highly diverged.
Reverse complement sequences are marked with "_R_" at the head of sequence title.
In the case of protein alignment, these options are just ignored.
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.