Why aren’t my fasta files importing correctly?

The FASTA file format is widely used, and many programs and databases have their own variations for how they format the header line to include information relevant to their data.  Geneious uses the standard format of the Fasta file description line.  This is to accommodate the wide variety of sources that generate Fasta files allowing Geneious to import Fasta files from any of these sources, not just NCBI.

The structure of a FASTA file is like this:

 >Name Description


with the sequence name (which cannot contain any spaces) followed by a space followed by the description.

Geneious uses this definition to parse the header line and find the sequence name and description when importing a FASTA file.  Thus anything after the first space will be imported into the “Description” column in the Geneious document table.  The name must not have spaces and if it does, they should be replaced with something like an underscore to keep the name as a single item.  Once the files have been imported, the underscore can be removed using ‘Batch Rename’ (Edit → Batch Rename).

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