You can load up the reference genome and reference annotation for any species and use those with any with every tool.
- The fasta is a Custom Reference Genome FAQ: How to use Custom Reference Genomes?
- and the database you create for it is a Custom Build FAQ: Adding a custom database/build (dbkey)
Instructions are in several posts with the tags custom-genome and custom-build
This recent QA is an example of the data retrieval and preparation steps → Inquiry about lettuce genome - #2 by jennaj
Hope this helps! 