I am trying to taxonomically classify two fungal genomes. I have read a couple ways to do this.
Align the genome to reference genomes using programs such as Mummer or Muscle, then build a maximum likelihood tree with RaxML.
Determine common orthologs with Busco or Cegma from the genomes and reference genomes, align and tree.
In your opinion, which is the best? Is there another way to taxonomically identify an organism from their genome?
Thanks in advance, Morgan