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.
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The former works well in most cases, unless the sequences are highly diverged.
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Reverse complement sequences are marked with "_R_" at the head of sequence title.
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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.
