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To export BLASt results as alignment select the results in the Annotations Editor and call the Export->Export BLAST result to alignment context menu item. The following dialog will appear:

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  <img src="/wiki/download/attachments/19759653/Exporting BLAST Results to Alignment.png"/>
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The following parameters are available:

Export to file - name of the new file.

File format to use - format of the new file. The following formats are available: CLUSTALW, FASTA, MSF, MEGA, NEXUS, PHYLIP Interleaved, PHYLIP Sequential, Stockholm.

Qualifier to use as name - name of the qualifier. The following qualifiers are available: accession, def, id.

Add reference to alignment - adds a reference to alignment.

Add document to the project - adds the new document to the project.

Select the options and click on the Export button.