====== 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.

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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**.

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===== Alignment =====

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

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===== Tree =====

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

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===== Quality management =====

Now you have two options to verify the results:

==== Single Sequence Blast ====

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

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==== Multiple Sequence Blast ====

Blast a whole fasta (BOLD login needed!):

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===== Create a fasta =====

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

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