I am using myRAST to annotate my sequenced genomes. How do I convert the outputs, .txt or .fasta into gff format?
If you only get a fasta output I'm afraid you cannot have easily a gff file. You should somehow align your fasta sequences against the genome to retrieve the position (and splicing if there is). You could use exonerate or GMAP to accomplish that.
But doing that you might loose some details.