Hello, I am attempting to use Sequin to prepare mitochondrial genome sequences for GenBank submission.
When I loaded my alignment into Sequin, I had one column that had all gaps, because the reference sequence they were aligned to (which I had removed from the fasta file) had an N base at that location.
Now that I have fully annotated one genome, the alignment validator is now telling me
ERROR: Segs: Segment 24 (near alignment position 3119) in the context of Y003 contains only gaps. Each segment must contain at least one actual sequence -- look for columns with all gaps and delete them.
The problem, however, is that it is unclear how to do this. I was wondering if someone could help me do this? Thanks