Improve aligning of a set of sequences to a reference sequence

Input data:
The data for the issue are on the file server.

Scenario:

1. Make sure MAFFT is set in the UGENE Application Settings.
2. Open "consensus.fa".
3. Convert it to an alignment to open it in the Alignment Editor.
4. Click "Align sequence to this alignment" button on the toolbar, browse for "Characiformes_all_cons_cluster_Majority.fasta".
   Current result: MAFFT is run like that:

   .../tools/mafft-7.212/mafft.bat --add fragment.fa alignment.fa
   

   The result alignment is too gapped with these input data and tool settings.

5. Unset MAFFT in the Application Settings.
6. Repeat steps 3-4 again.
   Current result: another custom algorithm is used to align the data. The result is alignment is better, although it may be further improved.

It is required to:

1. provide more options for aligning sequences to a reference
2. make it more clear how to use these options

See http://ugene.net/forum/YaBB.pl?num=1541689817.