Major In the following scenario the MAFFT algorithm, used in UGENE when aligning sequence to an alignment, does not work:
- There is an alignment of similar sequences.
- The added sequence is longer than the sequences in the alignment.
- First N characters (e.g. about 100) of the sequence do not match to characters of other sequences, the rest characters can be aligned well.
Current result: The sequence is not aligned well.
Expected result: Gaps are inserted at the beginning of other sequences. The other characters are aligned with the characters that match them.