--ep 0.123 → --ep 0.0
In comparison with the old default (--ep 0.123), the new default (--ep 0.0) allows longer indels and thus is more robust to unusual evolutionary events, such as domain-level indels. When little is known about the features of input sequences, the new default is safer, because less likely to make serious errors. Alignments by the new default are generally longer than those by the old default.
For small-scale data,
% mafft-ginsi --ep 0.123 input > output
For large-scale data,
% mafft-fftns --ep 0.123 input > output
For a large number (>∼20,000) of sequences,
% mafft --parttree --ep 0.123 input > output