We are sequencing an animal genome and the produced GFF file is version 2. However, I learned that GFF2 is now deprecated and GFF3 is a better choice. So I want a GFF3 file for the genome. Since I am not in charge of GFF production, I want to ask some questions here before submitting my request to the research group.
My questions are (1)How is GFF3 file produced? Is it difficult to get GFF3? Does it take much effort? (2) What softwares are available that support GFF3? GMOD mentions that Apollo, Chado, CMap and GBrowse support GFF3. Softwares based on Chado such as Artemis and ACT also support. Any more?