Generate Consensus Sequences

So if your alignment is clean and gap-free, mark all your assemblies and right click on Generate Consensus Sequence and adopt the settings below.

Move the consensus sequences into the separate folder Consensus within your plate folder.

There is also the cool option to edit the sequences names in a batch which I usually use at this point. As long as you have the FIMS-LIMS connection via the Biocode plugin you can put any column of field information in the name of the sequence. Use the AccessionNumber plus Taxonomy separated by an underscore as standard.

For changing sequences names in a batch click on Edit and then on Batch rename.

After renaming, mark all consensus sequences and right click on Alignment, but this time use the following options:

Mark the Nucleotide alignment, right click on tree and choose the following options:

Now you have two options to verify the results:

Blast barcodes one by one by copying each into the BOLD search:

Blast a whole fasta (BOLD login needed!):

For exporting a fasta, just mark all relevant consensus sequences, click on File → Export → Documents and choose *.fasta as format.