I'm trying to transfer annotations from an ancestral fungal genome to newly sequenced mutants, and for both speed and consistency I'd like to be able to transfer annotations from the ancestor to syntenic regions on the mutants. I've looked at Rapid Annotation Transfer Tool (RATT) and tried using their eukaryotic codon settings, but the coverage on each of the contigs is spotty - it seems to work well for the first 3rd of each contig and then fail for the remaining 2/3's, while claiming to complete successfully without any errors.
Does anyone have suggestions on other tools for annotation transfer / liftover that are explicitly designed to be used for eukaryotic genomes? At current the omictools directory only lists new annotation pipelines and not transfers. Thanks in advance,