Hi,

Since cegma has been discontinued, I have started using BUSCO. Previously to use Maker, in the maker.opts file: I used snaphmm=(file generated from cegma2zff, forge, fanthom, hmm aseembler). I ran Augustus separately and used the species file in augustus_species flag.

Can somebody please explain what file should I pass in the 'snaphmm' flag used in Maker form BUSCO analysis? Should I ignore the flag or is there any other way to generate snaphmm files from BUSCO analysis?

Thanks