I often want to import a SAM files to Geneious (v9.0.5). However, I always get a message saying 'Geneious can't find all the sequences it needs in the selected file.' followed by options to 'import as blank sequences', 'use the selected sequences', 'find sequences with the same name in this Geneious folder' or 'get the sequences from a file'.
What can cause this issue? It's annoying, because (1) I always need to import the reference sequence separately, (2) I get a manadatory row of '?' (blank sequence) in my alignment view. There is nothing wrong with my SAM files as far as I'm aware, so what's Geneious' problem?