Install Roary and Prokka
Go to path with fasta genomes
> cd path/to/fastas/
Annotate fasta genomes with Prokka
> for i in *.fa; do prokka $i --addgenes --locustag ${i%.*} --force --cpus 32; done
Collect all GFF files from each genome folder to tm folder
> mkdir tm && find . -name "*.gff" -type f -exec cp {} ./tm \;
 Copy files to roary folder
> cp path/to/tm/* path/to/roary
Run roary to produce core genome alignment
> roary -e --mafft -p 32 *.gff
Or just comparison
> roary -p 32 *.gff
If needed change the minimum blastp percentage identity. Its not advised to go below 90% unless you know what you're doing.
> roary –i 90 *.gff
Check the file gene_presence_absence.csv